The Gabon international, with 13 league goals this season, was suspended for last week's 0-0 draw with VfL Wolfsburg after failing to show up for a team meeting the day before.
Dortmund coach Peter Stoeger on Thursday indicated the 28-year-old would be in the squad but the forward was surprisingly left out with club officials saying he was not focussed enough.
Aubameyang, last season's Bundesliga top scorer, has been linked with a move to Arsenal in the January transfer window.
His absence was again clearly evident as Dortmund had few chances in a subdued first half before Davie Selke put Hertha ahead seconds after the restart.
Dortmund levelled by taking advantage of a defensive error when Shinji Kagawa headed in at the far post in the 71st.
The visitors could have snatched a late winner but Sancho curled his shot wide and Alexander Isak fired against the bar.
Dortmund have 30 points and trail Bundesliga leaders Bayern Munich who have 44 before they host Werder Bremen on Sunday.
Second-placed Leipzig on 31 visit Freiburg on Saturday.
(Reporting by Karolos Grohmann; Editing by Ken Ferris)
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