Bayern secured all three points against Mainz on Saturday afternoon, but the main headline was that Neuer was forced off shortly before half-time and replaced by Jonas Urbig.
The German champions have confirmed on Sunday that the legendary shot-stopper has "sustained a partial tendon tear in his right foot" as reports claim he will be out of action until January.
A tendon connects muscle to bone, and a partial tear means some of its fibres have been damaged, but the tendon has not completely ruptured.
For Neuer, a small partial tear can heal without surgery, while more extensive damage may require a longer rehabilitation programme.
Bayern have not officially confirmed a return date, but for now Urbig is set to play a major role until Neuer returns after the Christmas break.
The 40-year-old’s absence could hurt Vincent Kompany's title defence as his side enter the international break joint on points with Borussia Dortmund, separated by goal difference, as Bayern lead by 11.
Neuer is set to miss huge clashes with Arsenal and Sporting in the Champions League as well as Union Berlin in the DFB-Pokal.
Five Bundesliga clashes between those games mean Bayern must fight for 15 points without Neuer between the sticks in what may prove to be a struggle.