Musiala came on in the 57th minute against Boca Juniors. The nature of his injury wasn’t immediately known.
The 22 year-old had been recovering from a torn hamstring during the Bundesliga season.
Musiala had not played since April and returned to Bayern training on May 7.
Bayern and German national team coach Julian Nagelsmann decided not to name him to the squad during the UEFA Nations League semifinals in late May.
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