Bukayo Saka shone like a million stars in the game as Arsenal snatched a late win.
Aubameyang opened the scoring early in the game Cupido Congalves restored parity for Benfica just before halftime.
Benfica took the lead in the second half through Rafa Silva to out the visitors in front.
Kieran Tierney equalised for Arsenal before Aubameyang sealed their place in the next round with a cool finish.
Manchester United played out a goalless draw with Real Sociedad to book a place in the round of 16.
The Red Devils won the first leg 4-0 away from home to make the second leg a formality.
Leicester City lost 2-0 at home to Slavia Prague to crash out of Europa League.
AC Milan played out a 1-1 draw to advance on away goal rules.
According to Reuters, Ajax eliminated French Ligue 1 leaders Lille with a 2-1 victory in Amsterdam to complete a 4-2 overall win, while Gerard Moreno netted both goals as Villarreal dumped out Salzburg 4-1 on aggregate.
Egyptian forward Ahmed Hassan’s 88th-minute strike in Eindhoven sent Olymiapkos through at the expense of PSV 5-4 on aggregate, while Roma and Young Boys brushed aside Braga and Bayer Leverkusen respectively.
Former winners Shakhtar Donetsk completed a 3-0 aggregate victory over Maccabi Tel-Aviv, while Norwegians Molde dumped out Hoffenheim 5-3 on aggregate following a 2-0 win in Germany.
Dinamo Zagreb and Dynamo Kiev complete the line-up for the last 16, with Tottenham Hotspur also in the mix after destroying Wolfsberg of Austria by an aggregate score of 8-1 on Wednesday.