The German World Cup winner is believed to have suffered a hairline fracture during a recent training session at the club's Sabener Strasse base.
Now, it has been confirmed that the Bundesliga giants will be without their first-choice stopper until 2018 after he underwent surgery.
Chief executive Karl-Heinz Rummenigge told reporters: "We are very sorry that Manuel Neuer has injured himself again. The surgery went as planned, that's the most important thing right now.
"Together with our captain, we are looking ahead at the things to come. Manuel will be available as strong as ever in January."
The 31-year-old, who has suffered two similar fractures in the past six months, will miss the remainder of Bayern's Champions League group phase.