Anthony Modeste gave Hoffenheim the lead midway through the first half, but two goals from Claudio Pizarro and a Xherdan Shaqiri strike appeared to have given Pep Guardiola's men a commanding lead.
Hoffenheim had other ideas though and Sejad Salihovic pulled a goal back before the break before Roberto Firmino earned the visitors a point in the second half, making them only the third side to take anything off Bayern in the Bundesliga all season with a 3-3 draw.
Much-changed Bayern fell behind midway through the first half when Modeste raced from within his own half to latch onto Kevin Volland's searching ball.
Modeste's first shot was saved by Tom Starke, in goal against his former club to give Manuel Neuer a rest, but he followed through to ensure the loose ball went in.
Two minutes later, Bayern suffered another blow when Thiago had to be replaced by Philipp Lahm due to injury.
The champions regrouped and levelled in the 31st minute when Shaqiri's cross was headed in by the league's most prolific foreign marksman in history, Pizarro netting from close range.
Just three minutes later, the two combined in reverse order with Pizarro knocking the ball down for Shaqiri to net into the bottom left-hand corner.
Pizarro made it three five minutes before the break when he first spread the play for Franck Ribery, who delivered the ball back into the middle from the left for the Peruvian to guide in from close range.
It was a bit harsh on Hoffenheim, who had held their own well and caused the champions problems but they managed to reduce the arrears just before half-time when Salihovic curled a direct free-kick over the wall and into the top left-hand corner.
The visitors showed no fear and Firmino was denied by Starke early in what proved to be a wide open second half.
Hoffenheim, unsurprisingly the club who have conceded and scored more goals than everybody except Bayern this season, continued to cause the champions problems and their persistence paid off with Firmino pulling them level in the 75th minute.
After getting past Dante and Rafinha, the Brazilian picked his spot in the bottom right-hand corner from the edge of the penalty area.
Neither team wanted a draw, however.
Arjen Robben was denied by an excellent save from Jens Grahl while Tarik Elyounoussi sent a shot over the crossbar.
Sebastian Rudy wasted the last two chances for Hoffenheim, who came close to becoming the first side to beat Bayern in the Bundesliga all season, but only managed to take a point.