The versatile 24-year-old Spain international, who joined from Barcelona in 2013, suffered a severe knee injury that saw him sidelined for much of last season before coming back in April.
"We are happy that Thiago decided to stay at Bayern for the long term," said club CEO Karl-Heinz Rummenigge in a statement. "He is young and an important player for the future of the club."
Thiago, brought to Bayern by former Barca coach Pep Guardiola, has played 41 matches in all competitions for the Bavarians and also took part in both of this season's Bundesliga games so far as the club chases a record fourth straight league title.
(Reporting by Karolos Grohmann; Editing by John O'Brien)
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