The 23-year-old, who joined Bayern this season and was named in Spain's World Cup squad on Monday, has been out since March with a different ligament injury in the same right knee and was hoping to play in the Cup final against Borussia Dortmund on Saturday.
He underwent surgery and will remain hospitalised over the weekend, Bayern said. The creative midfielder is expected to be fully fit for the start of next season.
"This is bitter for Thiago and I feel sorry for him," said Bayern CEO Karl-Heinz Rummenigge.
"A young man who wanted to come back at the World Cup and suddenly his dreams are burst. We will take care of him now and make sure he is fit at the start of the season."
Thiago, who joined Bayern from Barcelona, underwent surgery shortly after his arrival back in August for damaged ankle ligaments that kept him out for months.
Spain, 2010 World Cup winners, have been drawn in Group B along with Netherlands, Chile and Australia.
(Reporting by Karolos Grohmann, editing by Ed Osmond)
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