Pierre-Emerick Aubameyang scored the opening goal midway through the half, clipping home after Bukayo Saka’s through-ball. Jan Vertonghen went close soon afterwards with a header over the bar for Benfica, but the Gunners had no reprieve minutes before half-time as Diogo Goncalves sent a brilliant free-kick into the top corner for the equaliser.
The Gunners had another Aubameyang finish ruled out for offside just after the break, before a terrible Dani Ceballos misjudgement saw his attempted header to Bernd Leno fall woefully short, with Rafa running in to beat the keeper and finish into an empty net.
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Arsenal then needed two goals to progress due to the Portuguese club netting twice in their away leg - although this game was in Greece and the first leg in Rome - and Kieran Tierney gave them the lifeline they needed with a fine solo effort, before Aubameyang popped up to head home another Saka cross in the closing stages.
Here are five things we learned from the game in Athens.
Auba’s shooting boots
The first meeting of these sides a week ago saw the Gunners’ main striker miss a hatful of chances, including the most jaw-dropping of misses with a side-foot effort from close range which was sent wide.
Arsenal should have been clear and leading after those sights of goal, but the first leg was all square; here, he showed no signs of repeating the unwanted trick.
His first real opportunity saw him instinctively dink a fine finish over the onrushing ‘keeper and in, while just minutes into the second half he also finished brilliantly, and also first-time, only for a VAR review to cancel out that one for the most marginal of offside calls.
No such reprieve for Benfica in the last minutes, though, as the striker headed in the all-important winner.
Gunners’ super Scot
Bukayo Saka had a very good start to the game, but the stand-out performer for Arsenal was unquestionably Kieran Tierney.
Defensively he had few problems, keeping pace with Diogo Goncalves and showing good positional sense to make several clearances tucked in narrow, while also making a few important interceptions to stop Benfica counters from deeper areas.
But it was again going forward where he really showed his importance to the team, not just with crosses and passes into the final third, but with a fierce determination and powerful running which the Portugues team struggled to cope with.
It wasn’t a surprise that Tierney was one of the main players trying to drag the Gunners to victory, with an unusually neat piece of footwork in the box and brilliant, drilled finish bringing the game back to 2-2.
Arteta’s obvious issue
Thomas or no Thomas, the centre of midfield is still a real issue for the Gunners.
Here it was blindingly apparent once again, but it’s hardly the first time: the Granit Xhaka-Dani Ceballos pairing is neither good enough on the ball to dominate matches, nor good enough defensively to stop the opposition slicing through at will.
Benfica were hardly the most direct and devastating team on the counter, yet found it very easy to pass through the pair when they did look to attack, Adel Taarabt, Pizzi and Julian Weigl swapping positions and making accurate, short passes around them.
A half-fit Thomas came on later but Ceballos had already done plenty of damage by then, with Xhaka particularly guilty of wasting possession in good attacking areas in the closing stages.
This is far from a vintage Benfica side, with the likes of Taarabt, Nico Otamendi, Jan Vertonghen and Pizzi all well past their prime - and not all of them elite-level talents to begin with.
They are fourth in the Liga NOS table - in habitually a three-horse race - after just one win in seven, and lack many of the usual bright prospects at present which have come through the ranks in previous years.
Over the course of two legs they were not, in truth, the match of Arsenal and the scoreline being so close until the latter stages owed more to individual errors at either end of the pitch than a real meeting of standards.
A period of rebuild is no doubt needed at one of Europe’s most famous old sides, with this being largely a season to forget.
With this win, however nervy, comes passage into the last 16 and Arsenal can now feasibly start to wonder how deep they can go into the competition.
Benfica were a good stepping stone between the absolute dross the Gunners faced in the group stage, and the other decent teams who will have aspirations of winning the Europa League itself.
Similarly, it’s pointless of Arteta and Co. believing they have shown they can lift the trophy just yet - if nothing else, the presence of Spurs, Man United and Leicester in the last 16, all teams ranked above Arsenal in the Premier League, shows they are not among the absolute favourites.
But each victory is a stepping stone toward where Arteta wants to take the team, a slow process which should help refine what aspects are repeated and which need to be improved. There’s still much work to do, but over two legs the Gunners should prove more dangerous opponents than they might be seen as in a one-off game, where their ongoing inconsistencies can still haunt them.