The 18-year-old has enjoyed a meteoric rise this season and is a serious contender for a spot on Germany's World Cup squad in May. The midfielder has scored five goals and delivered four assists in the Bundesliga alone.
"Lennart Karl has torn a muscle in his right rear thigh. The diagnosis was confirmed by the FC Bayern medical unit," the club said. "It means the 18-year-old attacking midfielder will be sidelined for the foreseeable future."
Bayern, nine points clear at the top of the Bundesliga with six games left to play, travel to St Pauli on Saturday.
They then host Real Madrid next week in their Champions League quarter-final second leg following the Germans' 2-1 win in Spain on Tuesday. Karl was an unused substitute in that game.
Bayern also face Bayer Leverkusen in the German Cup semi-final on April 22nd.