The Gunners suffered a 1-0 away loss in the first leg but overturned the deficit at home with a fourth-minute own goal from Zakhar Volkov - off Aubameyang's delivery - and efforts from Shkodran Mustafi and Sokratis Papastathopoulos.
The Gabon international who made his 33rd appearance this season in the encounter, featured for the entire duration but could not add to his 18 goal-haul.
However, the 29-year-old has taken to the social media to celebrate the victory while applauding the team for a job well done.
“Job done, [we] go to the next round,” Aubameyang posted on Instagram.
Arsenal will now shift attention to their next Premier League game against Southampton on Sunday.