Marseille's goalkeeper made several fine stops to prevent them falling further behind, including saving Mesut Ozil's penalty, but a second from Wilshere after the break secured the Londoners a 2-0 win.
They are not yet through to the competition's knockout stages, though, with Borussia Dortmund's 3-1 success over Napoli meaning that Arsenal's European fate will be decided in the final round of fixtures.
Below, you can read how the action unfolded, courtesy of Sports Mole's minute-by-minute coverage.
6.52pmEvening, all. It's a fairly simple equation for Arsenal this evening. If they beat Marseille, and Borussia Dortmund don't beat Napoli, they are through to the Champions League knockout stages.
6.55pmThe Gunners currently top the Group F table with nine points from their three games. Napoli trail them on goal difference, while Dortmund are three points back in the fight for last 16 qualification.
6.57pmYou can follow Dortmund's progress at the Westfalenstadion with Sports Mole, but here we are concentrating on Arsenal matters. Team news coming your way shortly...
7.08pmArsene Wenger makes three changes, half as many of the visitors, whose manager Elie Baup knows that even qualification for the Europa League via a third-place finish is highly unlikely.
7.10pmMathieu Flamini is recalled from suspension to play against his former club, with Mikel Arteta benched. Tomas Rosicky for Santi Cazorla is another swap from the weekend win over Southampton.
7.12pmFlamini's inclusion alongside Aaron Ramsey will likely mean that Jack Wilshere is shifted out to the right-hand side, where he has been forced to play much of his football since Mesut Ozil's arrival.
7.14pmArsenal's only other change sees Nacho Monreal replace Kieran Gibbs, who is omitted from the Gunners squad, at left-back. It is only the Spaniard's third start in all competitions this season.
7.16pmNicklas Bentdner is among the home substitutes despite being arrested on Monday, with police questioning the Denmark international for criminal damage to his Hertfordshire apartment block.
7.19pmThe want-away Danish international is joined on the Arsenal bench by Theo Walcott, who made his return from a two-month injury layoff with a 20-minute cameo against the Saints on Saturday.
7.21pmWenger will be hoping that there is an opportunity tonight for him to give the England international some more valuable playing time, to aid his recovery from an abdominal problem.
7.24pmAfter a run of seven winless matches, Marseille have picked up successive domestic victories, and they have indicated that Ligue 1 is their priority now by resting several star names tonight.
7.26pmReported Arsenal midfield target Florian Thauvin is only named on the visiting bench, as is France international winger Mathieu Valbuena and a handful of other first-team regulars.
7.29pmThere is a double change in defence as Benjamin Mendy and Souleymane Diawara drop out from the starting XI that beat Ajaccio on Friday, with Jeremy Morel and Lucas Mendes given starts.
7.31pmExperienced midfielder Benoit Cheyrou is benched, while Dimitri Payet, their second leading scorer in Ligue 1 this season, is given the night off completely. Mario Lemina and Gianelli Imbula come in.
7.34pmAndre Pierre-Gignac will be the focal point of the Marseille attack, and will have support from the flanks from two more recalled players, Jordan Ayew, brother of injured Andre, and Saber Khalifa.
7.37pmHEAD TO HEAD: Arsenal's record against Marseille should give them room for further confidence this evening. As well as their victory over the Ligue 1 outfit a couple of months ago, they avoided defeat to them in their two 2011 fixtures, when Aaron Ramsey bagged a 90th-minute winner in France.
7.40pmONE TO WATCH:Olivier Giroud is fresh off the back of a brace at the weekend and has been a much-improved performer for the Gunners this season. His link up play with Arsenal's attacking midfielders and goal haul has been impressive, and he shall hope to continue his good form tonight.
7.43pmPREDICTION: Everything points towards an Arsenal victory tonight. Marseille haven't been able to keep up with Group F's big guns this season and I anticipate that will be the story again at the Emirates. I'll plump for 3-0 to Arsenal, a result which may well be enough to see them into the last 16.
1 minWell, that didn't take long! Wilshere puts the Gunners in front after just 38 seconds, charging down the right before cutting inside, beating his man and bending a left-footed shot beyond the hand of diving Marseille keeper Steve Mandanda. What an incredible start. Arsenal are on their way already!
4 minNicolas N'Koulou is another Marseille man that has been linked with Arsenal. He will be looking to impress Wenger tonight, but won't do with passing like that, as he sends the ball crossfield and out.
7 minSAVE! Ramsey misses a gilt-edged chance to double Arsenal's lead inside seven minutes! Wilshere again cuts Marseille open down the right and this time squares for Ramsey, who has a tap in from eight yards, but Mandana spreads himself well and denies the Welshman with his trailing leg. Great stop.
10 minArsenal are wreaking havoc down the right flank, with Sagna getting forward at will. Wilshere finds him on the overlap, but the Frenchman's low cross is turned behind at the near post.
12 minUPDATE! Arsenal's qualification tonight depends on Dortmund failing to beat Napoli. However, the Germans are a goal up too, with Marco Reus giving them a 10th-minute lead from the spot.
15 minMarseille are doing their best to slow the tempo of this game down and prevent Arsenal scoring a second early on. They are content to keep the ball at the back, without forcing it forward.
16 minTheir patient possession yields a half chance for Gignac, as Ayew shifts the ball to Abdallah, who had made advances from right back. He crosses behind Gignac, whose 15-yard header loops wide.
17 minRamsey scoops a ball over the top of the Marseille defence for Ozil to run onto from the right channel, but the German's touch lets him down and the ball rolls off his foot straight to Mandanda.
19 minGiroud isn't quite on the same wavelength as his teammates so far tonight. He doesn't make a run to get onto Ramsey's flick around the corner, and his return pass to Rosicky is off the mark.
21 minCHANCE! The ball bounces off a couple of red shirts and falls kindly to Gignac in the box. He tries to round Szczesny, but his touch does not take the ball far enough away from Arsenal's Polish goalkeeper, who pinches the ball off Gignac's toes.
24 minAfter their electric start, Arsenal's attackers haven't quite been at it in the last 20 minute. Ozil pings a pass into the feet of Wilshere, who miscontrols the ball as he looked to turn towards goal.
26 minRosicky is popping up all over the place, but not to good effect at the moment. He drifts inside unchallenged off the left flank and shoots, but drags his 20-yard effort horribly wide.
29 minOzil's chip forward is headed clear by Mendes and falls to Imbula, who nearly puts his side in trouble by dawdling and allowing Wilshere to snatch the ball from him. It comes to nothing, though.
32 minArsenal fans shout for a penalty as Giroud is hauled to the ground by Mendes, but the Frenchman was offside from Ramsey's free kick so it is in fact Marseille who have the set-piece inside the box.
36 minPENALTY! Ramsey earns Arsenal a spot-kick with a lovely bit of skill, flicking the ball over the head of N'Koulou, who tripped the Welshman as he entered the area. The contact looked to be outside of the box, actually, but the Gunners won't complain! Ozil prepares to step up from 12 yards...
37 minSAVE! And he misses! The German, deputising for Mikel Arteta, Arsenal's usual penalty taker, stutters in his run up and then fails to get much power on his strike, which is really well saved by Mandanda! The Marseille stopper guesses the right way and strongly parries the ball away from danger.
39 minBOOKING: Mendes joins N'Koulou in being yellow carded for a trip on Ozil, for which Arsenal felt that they should have had another penalty. This time, though, the referee does deem the offence to be outside of the area, and awards them a free kick which Ramsey smashes straight at the wall.
42 minArsenal pass the ball along the 18-yard line, and it eventually comes to Wilshere, who may have opted to shoot on his right foot. Instead, he cuts inside looking for a repeat of his first-minute opener, but there is too much height and not enough dip on his shot, which flies harmlessly off target.
44 minThe Gunners are getting the ball back so easily at the moment. Marseille just aren't getting enough bodies forward to support Gignac, who is outnumbered five to one. No second Arsenal goal as yet, though, as we enter the ONE minute of stoppage time at the end of the first period.
8.36pmArsenal may be disappointed that this game isn't out of sight already. Jack Wilshere gave them the ideal start with a great individual goal after just 38 seconds, but it's been a bit toothless since then.
8.39pmAaron Ramsey had a fantastic opportunity to double Arsenal's advantage inside seven minutes when he was found unmarked eight yards out, but Marseille stopper Steve Mandanda made a fine block.
8.41pmThe French international goalkeeper came to his side's rescue again in the latter stages of the half when he saved Mesut Ozil's penalty, although it was a weak and lazy effort from the German.
8.43pmAS IT STANDS: The fact that Dortmund are matching Arsenal's 1-0 winning scoreline at the break against Napoli means that the Gunners would not guarantee qualification as it stands. Remember, they need to win and hope that last year's beaten finalists fail to beat Napoli at the Westfalenstadion.
8.45pmSTATS: The half-time figures echo my thoughts that the hosts should have this match wrapped up by now. They have enjoyed 70% possession, whereas Marseille are yet to have a shot on target or even a corner. I am sure Wenger will be urging his players to raise their standards after the interval.
46 minWe are back underway at the Emirates Stadium, with both sides unchanged...
48 minSome nice, quick passing between three or fours Gunners men on the inside left is eventually overcomplicated as Wilshere's back heel towards Ozil is intercepted by Lemina.
51 minSAVE! Ramsey goes into his bag of tricks and pulls out that scoop pass again, lifting the ball over the Marseille defence, beautifully into the path of Giroud. The Frenchman takes one touch on his knee to set up a volley which Mandanda punches away, before looking over to see the offside flag raised.
53 minThere are certainly signs of Arsenal moving the ball a bit quicker in this second half. Monreal plays a ball into Giroud's feet and then runs to get on the end of his clever return flick. The Spanish full back thinks he is unfairly shoved off the ball by N'Koulou, but in truth the defender was just too strong for him.
55 minCLOSE! Ozil follows Ramsey's example with a chipped pass over the top for Giroud, who lets the ball run across him before shooting on the half volley from 20 yards. His shot is deflected off the studs of N'Koulou, wrong foots Mandanda and comes within inches of sneaking inside the post!
56 minSAVE! Another lifted ball over the top, this time the pick of the bunch from Wilshere, finds Ozil's deep run from the right channel. The £43m man holds off the two Marseille defenders around him and then tries to prod across goal, but Mandanda forecasts this and gets down to make a good stop.
58 minSUBSTITUTIONS: Elie Baup introduces two of his big guns, Mathieu Valbuena and Florian Thauvin into the action, in place of Imbula and Ayew. Clearly the Marseille manager feels that while they are only one goal behind, they have a chance of nicking a result from this fixture.
60 minWilshere's perseverance while grounded in the box earns Rosicky a chance, and he feints a shot before eventually taking it on right footed, only for Mendes to stretch out a boot and block.
63 minMonreal sends in an early cross from the left which Giroud attempts to glance goalwards. The ball runs down his back and there is nearly a chance for him to prod at goal, before Mandanda claims.
65 minArsenal finally have the two-goal lead that their dominance warrants. Ramsey plays Ozil in between two static Marseille defenders, and the playmaker squares with the outside of his left boot for Wilshere to finish into the roof of the net from 10 yards. He has doubled his tally for the season tonight.
68 minUPDATE: Whatever you can do I can do better, or just as good, is the message from Dortmund. The Germans have taken a 2-0 lead over Napoli courtesy of Jakub Błaszczykowski's counter-attack goal.
71 minCHANCE! Full-back Morel makes a good run down the left and has four blue shirts up with him. He stands a cross up to Thauvin, whose header is too feint and flies some distance wide.
74 minOFF THE LINE! Just a few moments after Marseille threaten through Gignac, who had nearly been allowed in due to Rosicky's casual back pass, they force Szczesny into a fine save. Thauvin watches Valbuena's chip fall over his shoulder and volleys left footed, with Szczesny partially blocking the shot which is then cleared off the line by the retreating and aware Monreal.
75 minSUBSTITUTIONS: Wilshere's excellent evening comes to and end as Wenger pulls him off for the final 15 minutes. He and Rosicky make way for Santi Cazorla and Theo Walcott in a double change.
77 minSAVE! Szczesny shows the concentration needed in all great goalkeepers by pulling off a second good save in quick succession, after having nothing to do for 75 minutes! Again it is Thauvin who tests him, with a stinging left-foot drive which the Pole does brilliantly to tip around his post.
80 minWalcott uses his pace to get in behind and collect Sagna's lifted pass. Giroud is an option for him in the middle, but instead he cuts back towards Ozil, who is beaten to the ball by Morel.
82 minSUBSTITUTIONS: Both sides make their final change, as Benoit Cheyrou replaces Lemina for Marseille. For the Gunners, Arteta comes on for Ozil, a switch that will see Ramsey pushed forward.
83 minUPDATE: Napoli had pulled one back in Dortmund through Lorenzo Insigne, but Pierre-Emerick Aubameyang has since restored the hosts' two-goal advantage. They are on their way to victory.
86 minThe visitors have certainly asked more questions of Arsenal since Thauvin's introduction. You can see why the 20-year-old is admired by Wenger, and thought of so highly in general.
88 minCHANCE! Cazorla has an opportunity to add some gloss to the result after Walcott's fizzed cross was cleared straight to him, but his 12-yard left-foot volley was wild to say the least.
90 minCHANCE! Ramsey's back heel inside to Sagna leads to the Frenchman releasing Walcott through the middle. The substitute should use his left foot, but instead rustily toe pokes wide with his right.