Aubameyang completed a club-record £56million move to Arsenal on deadline day following weeks of negotiations.
His move saw Olivier Giroud head to Chelsea in a deal worth £18m.
Aubameyang will now be hoping to follow in the footsteps of Thierry Henry after inheriting the Frenchman’s No 14 shirt.
However, the Gabon international’s petulant behaviour in his last few months at Dortmund left a sour taste in the mouths of the supporters.
And Stoger has now revealed the effect Aubameyang’s move has had on the Bundesliga outfit.
“It’s good that it’s over because that issue occupied so much space in public,” Stoger told German paper Bild.
“Now there’s not that issue anymore behind which you can hide.
“In my time here (early December), he never came too late (to training).
“Only one single time he skipped our team meeting and only one single time he practiced badly because he want to put a sign [out], apparently.
“But apart from that he behaved reasonably.”
Aubameyang could make his Arsenal debut at home to Everton on Saturday (5.30pm).
The Gunners will be desperate to get back to winning ways after their 3-1 reverse away to Swansea in midweek.