The 28-year-old didn't emerge for the second half after suffering an injury during his side's meeting with Dortmund in the Allianz Arena
The shot stopper played all of the first half as his side went 1-0 down to their rivals on Saturday but didn't emerge for the restart, having been replaced by 20-year-old Lukas Raeder.
Neuer's absence was felt from the early stages of the second period as his young replacement conceded twice in the first 12 minutes, being caught in a poor position from Marco Reus and then seeing Jonas Hofmann smashing over him and into the back of the net shortly afterwards.
The injury could become a real problem for Pep Guardiola as they prepare to meet Real Madrid on April 23 in the semi-final of the Champions League and Kaiserslautern in the DFB-Pokal on Wednesday April 16. Bayern's second choice goalkeeper Tom Starke has been ruled out for the remainder of the season after tearing a ligament in his right elbow.