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The German giants were seeing a lot of the ball but midway through the half Anthony Modeste opened the scoring. His first shot after a run was saved, but he reacted quicker than Tom Starke to tap in the rebound.
However, Bayern were level inside 10 minutes. Claudio Pizarro met a Shaqiri corner to head in before the winger himself guided a neat effort from a Rafinha cross into the net to complete the turnaround.
It was 3-1 on 40 minutes as Pizarro finished off a good counter-attacking move, but right before the break Hoffenheim restored hope through Sejad Salihovic to cap a thrilling first half.
This time it was Hoffenheim's turn to come from behind as with 15 minutes left to play Roberto Firmino drilled a low finish beyond Starke to pick up a point for the away side.