The Gunners lost 2-1 after extra time at the Emirates Stadium on Thursday and that meant they were knocked out by their Greek opponents on away goals.
Aubameyang equalised with just six minutes remaining, only for Youssef El Arabi to score late on as the visitors qualified for the last 16.
But it would have had been a different story had Aubameyang, Arsenal's leading goalscorer so far this season, been on target with another chance soon after El Arabi's effort.
Aubameyang apologised after the game and Arsenal manager Arteta was pleased by the 30-year-old Gabon star's "mature reaction" to a desperately disappointing loss.