Spain's 30-man provisional squad is already down to 29 after Thiago's serious knee injury.
The playmaker had been hoping to make his return from injury against Borussia Dortmund in Saturday's German Cup final before injuring his knee in earlier this week. He will now undergo surgery, ruling him out for a substantial amount of time.
23-year-old Thiago was heavily linked with a move to Manchester United last summer, before opting to rejoin his former Barca manager Pep Guardiola at the Bavarian giants.
His first season at Bayern has been interrupted by injury, managing just 25 appearances, and his injury was on the same knee that has kept him out of action since March.
The midfielder has won five caps for Spain, though his most notable moment in a Spanish shirt was when he scored a hat-trick for the Under-21 side in the European Championship final last summer.
"This is bitter for Thiago and I feel sorry for him," said Bayern chief executive 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."
Spain will be seeking to become the first European team to win the tournament in the Americas, and will start the defence of their trophy in Group B against the team they beat in 2010's final, the Netherlands, before facing Chile and Australia.