Last weekend, Aubameyang was removed from the first-team squad due to disciplinary reasons, while reports continue to suggest that Arsenal are in negotiations to sign the forward before the end of January.
However, Stoger has suggested that no transfer is imminent, and that the Gabon international will likely feature against Hertha Berlin on Thursday night.
At a press conference, the 51-year-old said: "He wasn't an issue for us these last few days. We had a good, short talk on Monday. If nothing changes he's an option for tomorrow.
"Match practice is important for every player, maybe especially for younger guys. But for any club, particularly for a club like BVB, performances are the most important thing.
"I told Aubameyang what I want to see from him, that he gives it all in training. At the end it's up to him to qualify for the team and do what's necessary to be a part of it. Until I hear there's a personnel change he's part of my plans."