Diogo Goncalves levelled for Benfica just before the break with a superb free-kick after Dani Ceballos had needlessly fouled Julian Weigl.
The Spanish midfielder compounded that error after the interval with a poor defensive header that saw Rafa Silva race clear to put the visitors in front.
With Arsenal needing two goals to advance because of the away goals rule, Kieran Tierney’s low drive set up a grandstand finish before Aubameyang rescued the tie.
Mikel Arteta’s side will discover their last-16 opponents in Friday’s draw in Nyon (12:00 GMT).
Arsenal avoid another Greek exit
Having exited the Europa League at the same stage last season to Olympiakos, it looked as though circumstances had conspired for another European campaign to end in desperate fashion.
Faced with a four-hour flight for a fixture technically billed at home and inside a stadium where they have enjoyed mixed fortunes in the past, Arteta’s side started brightly enough.
When Aubameyang raced on to Bukayo Saka’s incisive pass to lift the ball beyond Benfica goalkeeper Helton Leite, they were firmly in control having drawn the first leg 1-1 in Rome’s Olympic Stadium.
But from that point the game began to unravel as Benfica scored from their first two efforts on target – thanks to a helping hand from Ceballos.
To their credit, though, the Gunners, who had won just one of their past six matches, displayed plenty of resolve to come back from the brink of a damaging defeat that would surely have left their hopes of lifting a trophy this season in tatters.
Tierney was rewarded for a fine individual display by becoming the first Scottish player to score in a major European competition for the club since 1980.
And Aubameyang, who came in for criticism after missing several chances in the first leg, atoned with his second of the night from Saka’s back-post cross.
Aside from sparing Arteta the inevitable questions over the club’s progression under his stewardship, it also provided the Gabon forward with an element of redemption after his last-gasp miss sealed their fate against Olympiakos 12 months ago.
Leno’s landmark – the stats
- Arsenal have reached the last 16 of the Europa League in three of the four seasons they have appeared in the competition, with the only exception being in 2019-20 (eliminated at the last 32).
- Benfica suffered their first Europa League defeat since February 2020 against Shakhtar Donetsk (2-1), ending their eight-game unbeaten run in the competition.
- Pierre-Emerick Aubameyang has scored in seven of his past eight cup matches for Arsenal (10 goals in total – FA Cup – five, Europa League – four, Community Shield – one), only failing to net against Benfica in the first leg during this run.
- Only Trent Alexander-Arnold (20) has more assists among English players for Premier League clubs in all competitions since the start of last season than Bukayo Saka (18), following his two assists this evening.
- Kieran Tierney became the first Scotsman to score for Arsenal in a major European competition since Willie Young against Gothenburg in March 1980 in the Cup Winners Cup quarter-final.
- Bernd Leno made his 100th appearance for Arsenal in all competitions, becoming the fifth German player to reach this milestone for the club after Jens Lehmann (200), Per Mertesacker (221) Mesut Ozil (254) and Shkodran Mustafi (151).