Aubameyang levelled the scores by bundling home from close range but the shock loss for Peter Bosz's men leaves them without a win in eight league games and 13 points behind league leaders Bayern Munich.
The 27-year-old striker had equalled the record in Dortmund's Ruhr derby collapse from 4-0 up against Schalke to draw 4-4, with his Bremen goal taking him to 97 Bundesliga strikes.
Aubameyang's new record was previously held by Tony Yeboah, the Ghana striker who played for Eintracht Frankfurt and Hamburg either side of a spell in the Premier League with Leeds United.
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