Shinji Kagawa salvaged a 1-1 draw at Hertha Berlin when he capitalized on a rare defensive lapse from the otherwise well-organized home side with 20 minutes remaining.
"We have to live with the point," said Dortmund coach Peter Stoeger, whose side missed the chance to go second ahead of the rest of the 19th round.
Hertha frustrated the visitors for long periods and Dortmund clearly missed Aubameyang's pace to create goalscoring opportunities.
The Gabon player, who was dropped from the squad for Dortmund's 0-0 draw with Wolfsburg last Sunday, was again omitted for what sporting director Michael Zorc said was a "sporting decision."
It was the third time in just over a year that Dortmund dropped the player for disciplinary reasons.
Davie Selke fired Hertha into the lead right after the interval. Valentino Lazaro played a one-two with Ondrej Duda and then sent in a low cross for Selke to convert at the far post.
Christian Pulisic forced a good save from Thomas Kraft as Dortmund sought a response, before a Hertha mistake allowed Kagawa to head in the equalizer.
Dortmund pushed hard for a winner but Hertha held on.
"We're satisfied with the point," said Hertha coach Pal Dardai, whose side remained unbeaten at home by Dortmund for the fourth game.
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