The former FC Barcelona midfielder, who had been named in Spain head coach Vicente Del Bosque's provisional 30-man World Cup squad, underwent a successful operation on the injury on Thursday morning.
'A bitter blow'
"It's a bitter blow for Thiago," explained Bayern chief executive Karl-Heinz Rummenigge. "We all feel really sorry for him. He's a young lad who's been working hard on his comeback and towards the World Cup in his father's homeland - and then it's suddenly all taken away from him. We'll really make sure we look after him in the weeks ahead and do everything we can to get him fit for the start of the 2014/15 season."
Various ankle and knee complaints restricted the 23-year-old to just 16 league appearances over the course of his debut Bundesliga campaign, with his last run-out coming against 1899 Hoffenheim on Matchday 28.