Pierre-Emerick Aubameyang scored twice — including an 87th-minute winner — to lead the Gunners at the Georgios Karaiskakis Stadium in Greece, which was serving as Arsenal’s home venue due to COVID-19 travel restrictions.
Benfica evened the aggregate scoreline two minutes before half-time through a sensational Diogo Gonçalves free kick after Julian Weigl was fouled at the edge of the Gunners’ box.
Benfica added a crucial second away goal just after the the hour mark thanks to a shocking error by Arsenal midfielder Dani Ceballos, who sent his backwards header directly into the path of a galloping Rafa who expertly rounded Bernd Leno and fired into an empty net.
The goal meant Arsenal needed two more to advance in the tie.
Kieran Tierney got one back soon after with a fine strike from the edge of the box after some nifty footwork to create space, and Aubameyang completed the comeback with a fine header from a Saka with three minutes remaining.