The Arsenal-linked striker was included from the off in Saturday's clash at the Westfalenstadion - his first appearance for the club since mid-December after being overlooked for selection by his manager.
Stoger vowed to give Aubameyang a chance to put his much-publicised disciplinary problems behind him against Freiburg, but the 28-year-old managed just one shot, one key pass and one touch in the opposition box during his 90 minutes on the pitch.
"I would say he has had better games," Stoger said at his post-match press conference. "On the one hand, it certainly wasn't his best game but, on the other, we didn't manage to give him decent service. In the end, he is part of a larger group of players who didn't have their best performance."