The Gabon player, who was dropped from the squad for Dortmund's 0-0 draw with Wolfsburg last Sunday, was again omitted from the side that drew 1-1 at Hertha Berlin.
"It's not a suspension but a sporting decision," Dortmund sporting director Michael Zorc told Eurosport before the game.
Dortmund clearly missed Aubameyang's pace to create goalscoring opportunities against Hertha's well-organized defense.
Zorc said there had been no offers made for the forward, who has been linked with a winter transfer to English side Arsenal.
"We're still planning with Aubameyang," Zorc said. "There is a way back into the team. Professionalism is part of that and also saying in one or two situations that a mistake was made."
Aubameyang was originally dropped for missing a club appointment, with coach Peter Stoeger saying he felt the player was "not so focused at the moment."
Zorc said he didn't know what the striker was thinking. It was the third time in just over a year that Dortmund has omitted the player for disciplinary reasons.
Aubameyang was dropped in November for inviting a film crew to the club and then turning up late for training. Former coach Thomas Tuchel also banned him 12 months earlier for taking an unsanctioned trip to Milan.
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