The Gabon international salvaged the Gunners from the jaws of defeat with his late goal at the Georgios Karaiskakis stadium in Greece.
After the first leg which ended 1-1 at the Stadio Olimpico in Rome, Arsenal needed to get a favourable result in order to progress to the next round at the expense of Benfica.
Aubameyang put Mikel Arteta’s men ahead just 21 minutes into the game, but Diego Goncalves equalized for Benfica, before Rafa Silva gave them a rare lead on 61 minutes.
Defender Kieran Tierney pulled parity six minutes later but the English side were starting down the barrel of elimination before Aubameyang popped up to head home a sumptuous cross from Bukayo Saka during the dying embers to send Arsenal to the Round of 16 stage.
“Solid! I have to tell the truth!” the captain said to the club’s official website.
“It was a hard one, but at the end I think we deserved it because we showed great character tonight, all the team and the guys that came in as well. They gave so much for the comeback and we did it, so we are so happy!”
“It’s hard because when you concede one, it’s okay, but then when you concede a second one, you know that you have to score two goals again, so it’s really hard, but as I said, we showed character and we kept calm during the whole match. We scored in the last minute and we are happy.”
“It could be very good [for the rest of the campaign]. I think in this difficult season, hopefully this will give us some hope, but also some confidence for the future that we can do comebacks like this.”
Aubameyang has now scored 13 goals in 26 appearances in all competitions for Arsenal so far this season.