Midfielder NuriSahin, who came from England after an unsuccessful loan spell at Liverpool, also netted two goals for Dortmund -- who will play Spanish side Malaga in the Champions League quarterfinals.
Former Bayern defender Mats Hummels headed the hosts ahead in the 10th minute from Nuri Sahin's free-kick, but Mario Gomez leveled 10 minutes before halftime as the striker made up for an earlier miss from Arjen Robben's cross by netting from close range.