Neuer was taking some time off after Germany suffered a group stage exit at the 2022 FIFA World Cup in Qatar.
The 36-year-old played 16 times for Bayern Munich across all competitions before the season went on a break for the World Cup.
In a post on his Instagram feed on Saturday, Neuer said: "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."
The news will come as a big blow for Bayern Munich who lead the Bundesliga table by four points and meet Paris Saint Germain in the round of 16 of the UEFA Champions League in February.
The Bayern Munich hierarchy have been reacting to the unfortunate news.
CEO Oliver Kahn said: "The news of Manuel's injury shocked us all. We will stand by him and accompany him on his way to his comeback.
"He will also overcome this serious injury and return to the pitch as strong as before."
In a statement on the club's website, sporting director Hasan Salihamidzic said: "The fact that Manuel had such an accident is terrible, and of course all our thoughts are with him.
"I spoke with him yesterday and today, and the surgery went as well as possible. Manuel will receive all the support he needs.
"He is a strong personality and will come back. I wish him all the best, he can rely on FC Bayern!"
Sven Ulreich is likely to deputise in Neuer's absence.
