Mouctar Diakhaby handed the Spanish side an early lead at Emirates Stadium but the Gunners levelled matters 14 minutes later through Alexandre Lacazette.
The Frenchman put the Gunners ahead seven minutes later before Aubameyang handed Unai Emery’s men a solid first leg advantage with his late effort.
28 – Pierre-Emerick Aubameyang has been directly involved in 28 goals in his 27 starts for Arsenal at the Emirates Stadium in all competitions (22 goals, 6 assists). Wakanda. #ARSVAL pic.twitter.com/IUTIIpGTbh— OptaJoe (@OptaJoe) May 2, 2019
The duo would be hoping to play a part when they welcome Brighton and Hove Albion in the club's penultimate Premier League game of the season on Sunday.