Defender Shkodran Mustafi had previously opened the scoring for the hosts with an eighth-minute header, and Henrik Mkhitaryan sealed the win with a 77-minute third.
The result ended Arsenal's run of three successive league defeats and should help them build momentum following Thursday's Europa League victory over AC Milan.
Relive how the action unfolded in North London with our minute-by-minute updates below.
12.30pmArsenal's season was threatening to spiral out of control before Thursday's Europa League win at AC Milan. Can the Gunners now show the cojones to back up that performance with a first Premier League win in four, against a Watford side who got one over on them back in October? Here's the team news...
12.36pmArsene Wenger makes the interesting decision to make six changes from the team which won in Milan in midweek, signalling that his priority is next week's second leg against the Italians. With a 13-point gap to Tottenham in fourth, this is a concession from the Frenchman that their top-four race is run.
12.40pmMohamed Elneny comes in for only his seventh top-flight start of the season in midfield, while Rob Holding, who has only begun two league matches in 2018, and Ainsley Maitland-Niles are drafted into a defence which Troy Deeney and Watford will fancy unsettling again this afternoon.
12.42pmDespite all of the changes, Wenger still fields a strong front four, with Mesut Ozil and Henrikh Mkhitaryan sitting in behind Aubameyang. Alex Iwobi is the player who benefits from the rotation with Alexandre Lacazette's ongoing injury preventing him from getting a chance to impress.
12.44pmFull-backs Hector Bellerin and Nacho Monreal are also in the treatment room, but Saed Kolasinac has overcome the knock that forced him off against Milan to start on the left of a flat back four.
12.46pmJavi Gracia makes just the one change from the Watford side which beat West Brom 1-0 last time out, with Kiko Femenia making his first league start in three months in place of Andre Carrillo. That gives the Hornets the flexibility to switch between a back three, or go with the Spaniard on the right wing.
12.48pmOrestis Karnezis, on loan from Udinese, has retained his place in goal since Heurelho Gomes returned from injury, thanks to three clean sheets in five matches. Watford's long-standing number one is not even on the bench today because of personal reasons, with Daniel Bachmann deputising.
12.50pmHis match-winning assist against the Baggies is not enough to earn Will Hughes a start as Gracia sticks with the partnership of Abdoulaye Doucoure and Etienne Capoue, which have the physicality and presence to overpower Arsenal if their midfield is as brittle as it has been in recent times.
12.52pmTom Cleverley, who scored Watford's stoppage-time winner in their win over Arsenal at Vicarage Road, has returned to training with the Hornets following a thigh injury, but this game comes too soon for him. Younes Kaboul, Craig Cathcart and Nathaniel Chalobah are long-term absentees.
12.54pmDespite the Brazilian's run of 18 matches without a goal, Gracia keeps faith in Richarlison on the left wing although that might be an enforced selection with January loan signing Gerard Deulofeu having picked up an ankle knock. Andre Gray is an alternative who has so far been ignored by Gracia.
12.56pmWatford skipper Troy Deeney will be the pantomime villain at the Emirates today following his provactive comments after his side's victory in October, accusing the North Londoners of lacking "cojones" after folding in the final minutes. In his defence, Arsenal's recent form has proved him right.
12.58pmThe Gunners have been beaten in five of their last seven matches in all competitions, including their last three league matches. They have never suffered four successive league defeats in Wenger's 23 years at the club, last doing so in March 1995 when Stewart Houston was manager.
1.00pmIt has been 11 top-flight matches since Arsenal kept a clean sheet, which is their worst run of the Wenger tenure and since they conceded in 12 straight games between April and October 1988. Goalkeeper Petr Cech, still searching for his 200 PL shutout, has shown his age in recent weeks.
1.02pmThis season's numbers continue to reflect poorly on the current state of Arsenal. They have lost 10 league games this term - which has only happened once over the last 12 years across an entire season.
1.04pmHaving begun the campaign with seven straight home league wins, Arsenal have won just three of their subsequent seven top-flight games at the Emirates, drawing two and losing two.
1.06pmArsenal are handed a lifeline today in the form of Watford's away record. The Hornets have drawn one and lost six of their last seven away league matches, scoring just twice during this run.
1.08pmThe Hornets have been particularly bad on short trips to the capital. Since beating Arsenal 2-1 in January 2017, Watford have lost six straight league games in London, conceding 17 goals.
1.10pmHowever, Javi Gracia has arrested the slide that cost Marco Silva his job and returned Watford to the top half of the table with a run of three wins in four matches, and only one defeat in five.
1.12pmA third successive Premier League victory this afternoon would be the first time that Watford have managed such a feat since December 2015, when they managed four wins in a row.
1.14pmOne thing that Gracia has done is restore Deeney as a regular starter, and his captain has rewarded him by scoring three goals in four matches, all of which have resulted in victories.
1.16pmSTAT: Impress/bore your mates at the pub tonight with this one. The last time that a team won three straight Premier League games 1-0 with the same player scoring each time was Liverpool's Daniel Sturridge in September 2013 - something which Deeney can achieve this afternoon.
1.18pmIf Deeney is indded the match-winner again, Watford would become only the third side to win back-to-back away Premier League games at the Emirates, after Chelsea in November 2009 and Swansea in March 2016. Last season they came away 2-1 victorys, with Deeney on the scoresheet.
1.20pmWatford's new defensive resolve under Gracia faces arguably its biggest test this afternoon. The Gunners have scored in each of their last 11 games against the Hornets in all competitions.
1.22pmAubameyang should be desperate to make an impression today, having been slightly underwhelming since his £60m arrival from Borussia Dortmund. He has scored two goals in five games but failed to show up when it mattered - in the big games against Tottenham and Manchester City.
1.24pmThis fixture has the honour of being the last to be commentated by the legend that is John Motson. Happy retirement Motty! Let's hope these two can produce an send-off to remember.
Legendary commentator John Motson will deliver his final live BBC commentary this weekend when Arsenal face Watford in the Premier League lunchtime kick-off on Sunday. #ARSWATpic.twitter.com/JLXIIeYcL1
1.26pmThere were some very unsavoury scenes at the London Stadium yesterday as West Ham fans invaded the pitch to confront players and the club's co-chairmen. Arsenal fans are upset at their own hierarchy and seem to be protesting with their feet, with the Emirates far from full as we approach kickoff.
1.28pmPREDICTION: If this game was at Vicarage Road rather than the Emirates than I would fancy Watford to restore Arsenal to misery, but the Hornets' away form is poor and there is plenty of quality in that Arsenal front four to get them over the line with a 3-1 victory today.
1 minKICKOFF: Arsenal get the action underway, with Martin Atkinson today's referee...
3 minCHANCE! Ozil creates a great early opportunity for Aubameyang by releasing him down the right channel. The Gabonese striker tries to fire a powerful shot through Karnezis, who gets just enough of his body behind the ball to deflect it behind for a corner.
5 minAn early ball up to the chest of Deeney prompts the attention of three Arsenal players as they surround the striker and easily rob him of possession. The Watford skipper has certainly made himself a target with his public criticism of the Gunners, but he won't shirk the battle.
6 minSHOT! Pereyra turns nicely and slips Richarlison through but the Brazilian fires into the side-netting.
8 minArsenal make the ideal start, and the goal is as simple as you like as Ozil swings in a wide free kick which Mustafi meets with a well-directed header, very similar to the one which he scored against Spurs earlier this season, after being allowed to run in between two Arsenal defenders.
10 minThat might kick Watford into life as the visitors had made a sluggish start. Janmaat bombs forward down the right but his cross and the subsequent corner are both cleared by Holding.
12 minSAVE! Pereyra flights a lovely ball over the top for Richarlison, who lets the ball run across him rather than taking a touch, allowing Mustafi to usher him wide. The Brazilian tees up Doucoure whose shot is saved by the reflexes of a Chelsea-like Petr Cech, reacting quickly low to his left.
14 minSTAT: Mustafi's goal was the 1,000th Premier League home goal for Arsenal, making them the second team to reach the milestone, after Manchester United of course.
16 minRicharlison requires some treatment for a head injury after an accidental clash with Elneny. This stoppage in play might help Arsenal as Watford had responded well to falling behind.
18 minCLOSE! Elneny is not known for his vision but he picks out the run of Kolasinac to the left byline, and his fizzed cross is just beyond the reach of Aubameyang at the back post.
20 minThe Egyptian midfielder is involved again as his cross eventually reaches Iwobi on the left edge of the box. He ignores the runs of several teammates to cut inside and bend a shot over the bar.
22 minThis time Elneny is guilty of giving the ball away in his own half, but Deeney tries to be too cute with his chip over the top towards Doucoure, when Femenia on the right was the better option.
26 minMISS! Watford waste a great chance to draw level as Cech pushes a Richarlison free kick right back into the danger zone, only for Pereyra to blaze the follow up from 12 yards high into the stands. More questions would have been asked of the veteran keeper had that gone in.
28 minSAVE! At the other end, Karnezis ensures that Watford's deficit remains at one with a crucial save to deny Ozil. The German international's perfect first touch takes him by Mariappa, and he tries to give Karnezis the eyes and reverse his shot into the bottom corner, but the Greek stretches out a leg.
31 minConcern for Arsenal as Ozil limps away from a nothing challenge with Capoue, puts the ball out of play and goes down to the floor. He may have been caught on the Achilles, which can be really sore ones, but the playmaker seems comfortable enough to try to run the injury off.
33 minIwobi needlessly strays offside while receiving an Ozil pass, despite looking right across the line. That is an opening wasted for the Gunners, who had men in the box and Watford on the ropes.
35 minWenger seems absolutely convinced about Xhaka being his holding midfielder, despite Arsenal's fans having serious reservations about his ability to protect the defence. Even with Elneny in the team today, the Swiss is the deepest lying of the two while the Egyptian is joining in attacks.
37 minOzil is taking up some dangerous positions between the lines and while Mkhitaryan has been quiet in comparision, the Armenian shows another side of his game here as he backtracks to muscle Doucoure of all people off the ball, and start an Arsenal break which is halted by Prodl's tackle.
39 minCapoue tries to set Pereyra away quickly after winning back possession in his own half, but Maitland-Niles comes across on the cover after the midfield runner had escaped Arsenal's centre-backs.
41 minCLOSE! The Hornets are having a good spell here, forcing Arsenal to defend their lead before the break. They work a corner nicely and Holding's interception from Femenia's cross deflects over Cech and lands on the roof of the anxious goalkeeper's net.
43 minThe confidence in this Watford team is definitely rising, as they pass the ball through Arsenal's midfield and spread it out to Janmaat, whose cross is too heavy for Deeney in the middle.
45 minHolebas takes a risk with a back-header for Karnezis, which only just reaches the goalkeeper under 'pressure' from Aubameyang, who might have been in had he been a bit braver.
2.20pmArsenal take a lead into the break thanks to Mustafi's early goal, but there is definitely something in this game for Watford. Even at the back end of that half, Richarlison forced a low save from Cech with a good header. The Emirates crowd are not comfortable with this narrow advantage.
2.22pmThe Gunners have had chances to extend their lead, with Karnezis saving from Aubameyang and Ozil, but the best chance fell to Pereyra when he skied a parried Richarlison free kick from eight yards.
2.24pmSTAT: On the 10 occasions that Arsenal have led at half time in the Premier League this season, they have gone on to win nine times, the only exception being at Watford in October.
2.26pmOne would have expected Deeney to be in the thick of things this afternoon but the outspoken Watford skipper has so far been shackelled by Mustafi and Holding. The home crowd have tried to make him a target too, although the Emirates might be as much as a third empty from where I'm sitting.
2.30pmBENCH WATCH: Andre Carrillo has been better as an impact player for Watford this season and is waiting in the wings to replace Femenia if Gracia wishes to be more adventurous. Wenger will keep things as they are for now and hope that his side can get a second goal.
46 minKICKOFF: The action resumes and immediately there is a nervy moment for Karnezis, who spills a 25-yard curler from Xhaka, nearly into his own net only to grab on the second attempt.
48 minHolding makes a crucial block from a Femenia volley which appeared to be heading for the bottom corner. The chance came from a couple of hopeful flicks from Doucoure and Richarlison.
50 minKolasinac's early-season promise appears to have abandoned him along with Arsenal's form. The left-back knocks a cross under no pressure straight behind for a goal kick.
52 minMustafi needs two bites at the cherry to stop Pereyra in his tracks down the Arsenal left after Mkhitaryan, whose use of the ball today has been poor, had given away possession yet again.
54 minIn contrast, Ozil has been a class above everyone else on the pitch. The German international always seems to have so much time on the ball and is dictating all of Arsenal's attacks.
56 minYELLOW! Mustafi becomes the first player to be carded at the Emirates today as he hacks down Richarlison down the Watford left. From the resultant set piece, Elneny has to be alert to block a cross from Femenia after another well-worked training-ground routine.
59 minGOAL! ARSENAL 2-0 WATFORD (PIERRE-EMERICK AUBAMEYANG)
59 minAgainst the run of play, it must be said, Arsenal get a much-needed second with their former Borussia Dortmund duo combining to perfection. Mkhitaryan times his through ball to perfection and Aubmayeng keeps his composure to round Karnezis and slot into the vacant net with his left foot.
61 minPENALTY! Just as Arsenal looked as though they had grabbed control of the game, they concede a penalty as Pereyra tricks his way past Maitland-Niles and forces a blatant foul in the box.
62 minSAVE! Deeney steps up and Cech saves down the middle, stretching out a left hand to prompt the biggest cheer of the afternoon at the Emirates! Maybe today is the day that Cech finally reaches his clean sheet milestone, and maybe the Watford captain will learn to keep his mouth shut.
64 minSUBSTITUTION: Will Hughes is on for Watford in place of Kiko Femenia. In his few Premier League appearances either side of injury, the former Derby man has shown that he has the ability to create chances at this level. Mind you, Watford won't have any bigger than the one they just had.
66 minYELLOW! A frantic period of play produces a rash tackle from Holebas on Mkhitaryan which sees him booked. The Armenian wanted a penalty moments earlier for a foul by Mariappa, who wiped out the Arsenal winger way after his cross had evaded Aubameyang in the box.
68 minSUBSTITUTIONS: Both managers make a change as Wenger swaps Iwobi for Welbeck, and Gracia brings on Stefano Okaka to partner Deeney up front, at the expense of Pereyra.
70 minMkhitaryan passes up a good chance to release Aubameyang again and runs into trouble.
72 minSUBSTITUTION: Wenger's second substitution is forced upon him as Mustafi picks up a knock while clearing a Holebas cross. It may only be a precaution but Chambers is on in his place.
74 minSome of the fight appears to have been taken out of Watford with that penalty miss. They were on top before Arsenal's second goal but the double setback has knocked the stuffing out of them.
76 minDoucoure attempts a difficult pass towards Okaka down the right channel. Surely with the Italian and Deeney to aim for, Watford's best chance is to get the ball wide and swing crosses in.
77 minGOAL! ARSENAL 3-0 WATFORD (HENRIKH MKHITARYAN)
77 minThe points are wrapped up for Arsenal with this third goal from Mkhitaryan. 'Yo Pierre' returns the favour by teeing up a left-footed shot which squeezes through Karnezis, who may have been blinded by the attempted block from Mariappa in front of him. Two in two now for the January signing.
79 minSUBSTITUTION: And that is the Armenian's final contribution as Wilshere comes on for the final 11 minutes.
81 minWith all of his substitutes used up, and considering how much he appears to rely on the Swiss midfielder, the sight of Xhaka going down clutching his ankle will be a worry for Wenger...
83 minDoucoure thwarts a chance for Wilshere to release Ozil for a potential fourth Arsenal goal by barging into the midfielder, and Martin Atkinson's well-meant advantage comes to nothing.
85 minThe ball nearly falls to Okaka in the box but Arsenal get enough bodies around the big substitute to restrict him to a tame poke which rolls harmlessly wide of Cech's goal.
86 minSHOT! Arsenal seem to have some of their swagger back and a lovely passing move eventually sets up a chance for Welbeck, whose shot is turned around the post by Karnezis.
88 minWatford appeal optimistically for a penalty after Chambers blocks Richarlison's run into the box.
90 min"Deeney, what's the score? Deeney, Deeney what's the score." Football fans have a great sense of humour.
90+1 minYELLOW! Xhaka picks up the most unneccesary caution for a shirt pull on Doucoure. There will be three minutes of added time for Cech to preserve his landmark 200th PL clean sheet.
3.28pmAll is not lost at Arsenal then, as they record back-to-back wins for the first time since January with a 3-0 victory over Watford. They are still 10 points adrift of the top four, which is out of their reach, but this result should give them confidence heading into their date with Milan on Thursday.
3.30pmThat's it from the Emirates Stadium as Sports Mole's attention switches to Arsenal's North London rivals Tottenham, who are in action at Bournemouth at 4pm. My colleague Barney Corkhill will guide you through that game. Thank you for joining me for this one this afternoon. Goodbye!