The German international was injured as he tried in vain to stop Cristiano Ronaldo from completing his hat-trick in the 4-2 Champions League quarter-final loss to Real Madrid on Tuesday.
After being 2-1 down from the first leg, Bayern took this game to extra time. Sergio Ramos netted an own goal a minute after Ronaldo thought he had scored the all important goal for Real, this after Robert Lewandowski had opened the scoring on the night from the penalty spot.
But a further strike from Ronaldo meant Real were safe, before he added a third, and Marco Asensio a fourth, right at the death.
A statement Bayern's website read: "Manuel Neuer suffered a fracture to his left foot in the 4-2 defeat away to Real Madrid according to an initial diagnosis.
"The Bayern goalkeeper sustained the injury during Cristiano Ronaldo's third goal in extra-time of the Champions League quarter-final return.
"Neuer will undergo a thorough examination on arrival in Munich prior to a decision on the appropriate treatment."