Aubameyang, the top scorer in the Bundesliga last season, was also dropped for last Sunday's goalless draw at home to Wolfsburg.
Dortmund coach Peter Stoeger took the decision to leave out the Gabon international again amid reports he is chasing a move to Premier League side Arsenal, who look set to lose forward Alexis Sanchez to Manchester United.
"There is nothing concrete on the table, only a lot of air," Dortmund director of sport Michael Zorc told 'Eurosport' when asked about the Arsenal rumours.
"We're planning with Pierre-Emerick Aubameyang and there's a way back into the team for him, but professionalism is part of that."
He continued: "That includes saying you've made a mistake in one situation or another."
Aubameyang is being disciplined by Dortmund for the third time in 16 months after he missed a team meeting last weekend.
Stoeger said the 28-year-old can still win back his place in the team for next weekend's home match against Freiburg.
"If he can help, he can offer himself up again. If he works hard in training, he will be back next week," said Stoeger.
Dortmund play Hertha Berlin on Friday.