The club did not specify how long de Ligt would spend on the sidelines, saying he was "out for the time being" and "will be missing from FC Bayern in the next games."
Bayern travel to rivals Borussia Dortmund on Saturday.
The Netherlands central defender injured his right knee as Bayern were eliminated 2-1 to third-division Saarbruecken in the German Cup on Wednesday night.
De Ligt, who has just returned from an injury to the same knee, grabbed his leg and signalled immediately to the bench 19 minutes into the match, before being subbed out.
Midfielder Joshua Kimmich moved to centre-back, with Bayern having only one fit central defender in the squad.
Bayern's French centre-back Dayot Upamecano has missed the club's last four matches with a hamstring injury.
Manager Thomas Tuchel confirmed after the match de Ligt's injury was to the "same knee" and "was extremely painful".
Bayern took the lead through Thomas Mueller after just 16 minutes, but their third division opponents equalised in first-half injury time.
With the scores locked at 1-1 and the game looking set to go to extra time, Saarbruecken's Marcel Gaus scored in the sixth minute of injury time to win.
The loss means 20-time German Cup winners Bayern have been eliminated in the second round in three of the past four years.
Bayern sit second on the Bundesliga, two points ahead of Dortmund, and have not lost a clash between the two sides since 2018.
