Four days before their Champions League quarter-final, first leg at Villarreal, Bayern put in a strong performance on the road.
However, there could be consequences for Bayern who briefly had 12 players on the pitch after a mistake following a late double substitution.
"We drew the referee's attention to the fact that Bayern had eleven outfield players on the pitch," Freiburg director Jochen Saier told 'Sky'.
"That was bizarre, I haven't seen that before." Freiburg need to lodge a formal complaint for there to be repercussions for Bayern.
Referee Christian Dingert noted the incident - which he described as a "totally confused situation" - in his match report and the official told Sky: "Now the DFB (German Football Association) must decide."