Manuel Neuer is likely to be out until 2018 after suffering a repeat fracture of a metatarsal on Monday. The goalkeeper has struggled with his fitness in recent seasons and was kept out of the Germany squad in September.
The goalkeeper suffered a foot injury while training in Munich and the club confirmed that he will be out for some time.
"Manuel Neuer has sustained another injury and we're incredibly sorry for him," said Bayern CEO Karl-Heinz Rummenigge .
"The operation went perfectly, whch is the most important thing for now. We and our captain are now looking to the future. Manuel will be back to his previous best and available to us again in January.“
Neuer, 31, returned from a four month injury layoff in August. He has played four games for Bayern this season since his return, the Bavarian club winning three of those four starts. He has missed 12 games for Bayern since the beginning of 2017 with various calf and foot ailments.
Despite his return, Neuer was kept out of the Germany squad for World Cup qualifiers against the Czech Republic and Norway. Germany coach Joachim Löw admitted he was trying to save his top goalkeeper, saying it would have been "fatal to put him at risk."
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Sven Ulreich, Bayern's back-up goalkeeper, is expected to start in Neuer's place. Ulreich, 29, has started 13 games for Bayern since joining from Stuttgart in 2015.
Bayern Munich each of the last seven games they have played in Veltins Arena in Gelsenkirchen. Neuer, who joined Bayern from Schalke in 2011, had started every game against his former club.