The 36-year-old was on holiday after Germany’s exit from the World Cup at the group stage but suffered the injury which needed surgery.
Neuer confirmed he will not play again this season.
He posted on Instagram: ‘What can I say, the end of the year could have definitely gone better… While I was trying to get my head clear while ski touring, I suffered a lower leg fracture.
‘Yesterday’s surgery went well. Many thanks to the doctors! However, it hurts to know that the current season is over for me.’
Neuer played all three games for Germany in Qatar as his side embarrassingly exited at the group stage for the second successive World Cup.
Bayern are currently locked in a battle for the Bundesliga title with Freiburg and comfortably reached the knockout stage of the Champions League, topping a group which included Inter and Barcelona.
The 2020 Champions League winners are due to face Paris Saint-Germain in the last 16 with the first leg scheduled to take place on February 14.
Despite a second successive group stage exit, meanwhile, Germany look ready to persist with Hansi Flick as their head coach.
Earlier this week technical director Oliver Bierhoff saw his contract terminated but Flick appears likely to remain in his position.
‘My coaching staff and I are optimistic about the European Championship in our own country,’ said Flick earlier this week.
‘As a team, we can achieve a lot more than we showed in Qatar. We missed a great opportunity there. We will learn our lessons from that.’
DFB president Bernd Neuendorf said: ‘We have full confidence in Hansi Flick that he will master this challenge together with his team.’
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