Papiss Cisse gave the home faithful some hope with 20 minutes left on the clock, finding the net after being set up by Shola Ameobi.
However, Benfica broke Newcastle hearts in stoppage time when Eduardo Salvio pounced and levelled the tie on the night.
Find out how all the action unfolded with out minute-by-minute commentary below.
7.10pmGood evening and welcome to our live text coverage of tonight's Europa League clash from St James' Park. Newcastle go into this evening's game trailing 3-1 from the previous leg. Find out how that unfolded here.
7.13pmIs this mission impossible for the Magpies? Not quite, but it is a steep mountain to climb given the quality of this evening's opposition. With the hosts possessing an away goal, the tie could well hinge on who draws first blood tonight.
7.22pmSUBS: Paulo Lopes, Cardozo, Aimar, Pereira, Rodrigo, Jardel, Andre Gomes
7.22pmLooks like Benfica will be going for the jugular tonight, opting for a three-pronged attack. The free-scoring Oscar Cardozo is a surprise omission from the starting XI. I'm not sure whether his inclusion on the bench is related to his fitness or purely tactical.
7.25pmAs we've already touched on, Newcastle have quite the task on their hands tonight. Benfica are virtually unbeatable domestically and have lost only to Barcelona in Europe this season. That away goal gives the hosts a glimmer of hope, but the odds are certainly against them.
7.28pmSome pre-match quotes from both managers coming up...
7.30pmALAN PARDEW: "There's only one team which has beaten them by two clear goals, and that's Barcelona. So that's the size of the task, so we are under no illusions there.
"This is a Champions League team, really, and if it weren't for Celtic's fantastic performance in the group, they could have been competing in the Champions League.
"That's the quality we are up against. I don't think there are going to be many better sides that have played here than Benfica."
7.35pmJORGE JESUS: "Newcastle will start off very strongly and play a more direct game, putting plenty of pressure on our defence. They've a number of players who are very strong in the air, like [Papiss] Cisse and [Shola] Ameobi, who I believe will start up front together, so we'll need to be prepared for that eventuality."
7.36pmWell the Benfica boss was wrong about one thing. Ameobi will not start up front this evening. He takes up a place on the bench, but is a dead cert to feature at some point.
7.39pmHistory is on Newcastle's side tonight. They have never lost against Portuguese opposition at St James' Park, winning four and drawing two of their six previous encounters. Their defeat in the first leg was only their third in 12 contests against teams from the country.
7.42pmNo team have kept more clean sheets than Newcastle in this season's Europa League, but Benfica have the best shot conversion rate in the competition. Make of that what you will.
7.45pmScoring goals is what Benfica does best, netting 23 in their last six competitive matches. You have to go all the way back to last October for the last time they lost, excluding penalty shootouts.
7.49pmTonight's match odds are: Newcastle 9/5, Benfica 6/4, draw 11/5.
7.51pmSo Benfica are the favourites to win on the night, according to the bookmakers. My money is on a score draw this evening, with Benfica progressing on aggregate.
7.54pmArgentine pair Ezequiel Garay and Nicolas Gaitan are ones to watch for the visitors this evening. They could well be playing in the Premier League this season, as Manchester United are rumoured to be keeping close tabs on them.
7.56pmFormer Chelsea man Nemanja Matic is another to look out for. He impressed during the previous leg in Lisbon and netted a goal against Olhanense in the league on Sunday.
7.58pmSome interesting comments from Alan Pardew on ITV just now. The Magpies boss has just admitted that he would take 0-0 with 20 minutes to go where he offered that now, stressing the importance of defending well and keeping a clean sheet.
8.00pmWhile a Benfica goal would surely kill off the tie, I think the Magies should be looking to draw blood in the first half. That way the pressure will be well and truly on the visitors.
0 minThe match is under way here at St James' Park. Chelsea booked their places in the semi-finals tonight. Can Newcastle join them? The next 90 minutes will reveal all.
2 minNewcastle content to hold possession in their own half in the opening stages. Cisse attempts to latch onto a long ball at the other end, but it is played too long, allowing Artur in the Benfica goal to calmly collect.
3 minCHANCE! Krul is the first goalkeeper to be tested this evening. Almeida played a cross in from the right and Lima met it with a wry flick, forcing the Magpies stopper to save with his legs.
5 minKrul is called into action again. He gets his fingertips to an effort from Lorenzo Melgarejo. I'm not sure where that was intended as a cross or shot, but it was dipping under the crossbar. Newcastle under the cosh in the early stages here.
8 minGaray and Cisse collide off the ball. That looked painful for both parties, but it is the Newcastle man who is still on the ground. He is receiving treatment, but should be back on his feet soon.
10 minNewcastle are seeing more of the ball now. Sissoko has just gone on a mazy run following some good team play, doing well to keep the ball in, but he does not have enough support up with him to keep the attack going.
12 minCabaye plays a long ball towards Haidara, but puts too much on it and it goes out of play. Bigirimana then tries to pick out Cisse with a ball over the top, which was inches from finding its target.
14 minBigirimana's through ball to Cisse is Newcastle best opportunity so far in what has been a nervy encounter. The midfielder demonstrated great vision to pick out his teammate's run, but it didn't quite come off.
18 minBenfica looking comfortable on the ball, but their keeper Artur has just gifted Newcastle a throw in in a dangerous position. This could be an opportunity to put the visitors on the back foot.
20 minThe throw comes to nothing, but Newcastle are soon pressing again as Cabaye plays a lofted pass over to Bigirimana on the right flank, only to watch his teammate overrun it and hand Benfica a goalkick.
22 minNewcastle have come out of their shell a little in the last few minutes, but have created nothing of any note. Benfica have just wasted a set piece at the other end after Enzo Perez was fouled by Bigirimana, sending the ball out for a goalkick.
25 minUPDATE: It's a good start for Tottenham in tonight's other Europa League fixture. They lead Basel 1-0 on the night and 3-2 on aggregate thanks to a goal from Clint Dempsey.
28 minOFF THE LINE! Krul is left stranded in no man's land and Gaitain rounds him and gains possession in front of the unguarded net. He pulls the trigger but Haidara pulls off goalline heroics to keep Newcastle in the tie!
30 minBOOKINGS: Enzo Perez is the first player to go into the book this evening for unsporting behaviour. Artur needlessly joins him on a yellow card after becoming involved in the aftermath.
32 minUPDATE: Basel have drawn level against Spurs. It's 1-1 on the night, with the Swiss outfit now leading on the away goals rule.
36 minCHANCE! John gains possession from Lima and goes on a surging run along the left flank. He plays a cross into Eduardo Salvio in the box, but it goes straight over his head and out for a goalkick.
37 minIt's Benfica who have done all the pressing tonight. Enzo Perez has just hit a snap volley from 25 yards, forcing Krul into another save. You wouldn't known it was Newcastle who need two goals to stay in the competition.
40 minAnother Newcastle half-chance goes begging as Bigirimana strays offside. Benfica are controlling the flow of the game, and look a cut above their hosts. Bigirimana hits a weak shot towards goal moments later. Artur gathers without any trouble.
43 minMuch better from Newcastle. Gutierrez makes a good run on the left side and whips a cross into the box, forcing Perez hack out from a Magpies flow. The home crowd are encouraged by what they have just seen.
45 minDISALLOWED GOAL! Bigirimana plays in a looping cross from the right that falls to the feet of Cisse in front of goal. The striker buries, but the linesman's flag went up moments earlier. The official's call was correct, but you have to feel for Newcastle!
8.57pmBenfica are a little unfortunate to not be ahead at half time. It took goalline heroics from Haidara to keep the scores level when Gaitain rounded Krul, but you could also argue that Cisse was only an inch or two offside when he found the net at the other end.
9pmThe Magpies are losing the midfield battle, which is allowing the visitors to control play. They need to shake things up in the second period, maybe make a change or two because it needs to be them doing all the pushing.
45 minThe match is back under way at St James' Park. Newcastle need two goals without reply in this second half to progress.
46 minThere was a change for Newcastle at half time. Gael Bigirimana makes way for Shola Ameobi. Benfica are the first to press in the second period with John playing a free kick into the hands of Krul.
49 minCabaye plays a free kick long into the Benfica box. Artur comes racing off his line and makes the catch without too much trouble.
50 minHalf-chance for Newcastle as Ameobi gains possession inside the area and attempts a cut back, the ball cannoning off a red shirt and going behind for Newcastle's first corner of the evening.
53 minJohn squanders a Benfica chance, putting an effort into the stand after collecting the ball in the Newcastle box. He had other options but went for goal himself. Wasteful play there.
55 minCHANCE! John and Gaitan exchange passes and the latter finds Salvio inside the box. He shoots first time, but blazes the ball over!
57 minA wasted opportunity for Newcastle at the other end. They were awarded a free kick in a shooting position, which Cabaye stepped up to take. He lifted his effort over the wall, but it was too high to trouble Artur. Newcastle won't get many better chances than that tonight.
60 minThe home fans are calling for Ben Arfa to be brought on now. They could do with his flare I think. Cisse just thought he had a shooting opportunity, but the offside flag quashed his attack.
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63 minNEWCASTLE SUB: The home faithful get their wish as Ben Arfa is brought on for Anita. There's plenty of time to score the two goals Newcastle need, but they haven't pressed anywhere near enough this evening.
66 minANOTHER DISALLOWED GOAL! Cisse puts the ball away again, but once again it is ruled offside. Ameobi provided the assist with a flick on, but was offside when he got the decisive touch.
67 minAnd Cisse receives a needless yellow card for dissent in the aftermath. A sign of Newcastle's frustration no doubt. The hosts have made their third sub now, with Massaido Haidara making way for Sylvain Marveux.
72 minBen Arfa catches the Benfica defence napping and cuts inside, playing the ball to Ameobi. He crosses in to Cisse in the centre of goal, and he heads home from close range. Game on!
73 minNewcastle need to throw the kitchen sink at their opponents now and push for that second goal, but they need to remain watertight at the back because the free-scoring Oscar Cardozo has come on for Lima.
75 minThe home crowd let their frustration be head as Cisse and Artur scramble for the same ball and the referee awards a goalkick. The replay shows that the Newcastle man did in fact get that last touch and the ref made the correct call.
76 minBENFICA SUB: Rodrigo comes on to replace John. Benfica are now playing with the same two strikers that Newcastle faced in Lisbon. And we all know how that turned out.
77 minBen Arfa cuts the Benfica defence down the middle with a well-time through pass, but there is too much on it for Marveaux to reach. Artur makes an easy claim.
78 minCisse nods down for Ameobi in the Benfica box, but the latter fails to stay on his feet. Newcastle haven't created any clear-cut chances since going ahead, but they are the ones doing all of the pressing now.
81 minBenfica get back on the front foot with Cordoza dancing his way around the Newcastle defence. Yanga-M'Biwa eventually brings him down 30 yards out and is booked for his challenge. Garay smashes the resultant free kick wide of the target.
83 minUPDATE: Spurs are at 2-2 in Basel now and that one is heading for extra time.
83 minMeanwhile, Williamson is booked for a shirt pull. No shortage of yellows here at St James' Park tonight.
85 minSHOT! Gaitan exploits poor defending from Newcastle, gets in between two defenders and lets fly. Krul saves low to his right.
88 minDanny Simpson ventures forward along the right and plays a chipped cross into the box towards Ameobi, but there was some shirt-pulling in the area on Newcastle's part. The move breaks down as the referee blows for a foul.
89 minCHANCE! End-to-end action in the latter stages here. Krul saves from Gaitan at point blank range at one end, and Ben Arfa blazes the ball over at the other.
90 minFour minutes of stoppage time for Newcastle to score the second goal they need. They have a free kick in a good position now...
90+2 minCabaye shoots from almost 30 yards out. It takes a deflection on the way, but Artur makes a comfortable save in the end.
90+2 minNewcastle United 1-1 Benfica (Eduardo Salvio)
90+4 minNewcastle have been caught on the break, moments after going for goal from a set piece. Benfica played a devastating counter-attack, which ended with Gaitan playing a low cross into Eduardo Salvio in front of goal, and the striker confidently placed his shot beyond Krul to fire Benfica into the semi-finals.
10.00pmThere goes the final whistle and Newcastle bow out of the Europa League despite tonight's valiant effort. There's no denying that Benfica deserved it over the two legs. I think they are genuine contenders to go all the way this year.
10.02pmThat's all from me here tonight, but stick with Sports Mole for match analysis and all the fallout from tonight's games. You can read our match report here.