Boateng, 31, was replaced during the first half of Sunday’s 1-0 victory in Lisbon, having been declared fit days after straining his hamstring in the semi-final win over Lyon.
Bayern said Tuesday the centre-back will complete a rehabilitation programme prepared by the club during his holiday but gave no indication as to how long he is expected to be sidelined.
Boateng has rediscovered his best form under Hansi Flick alongside David Alaba at the heart of Bayern’s defence, helping the club to a second treble of Bundesliga, German Cup and Champions League titles in seven years.
Bayern kick off their 2020/21 season against fifth-tier outfit Duren in the first round of the German Cup on September 11. They then host Schalke in the opening game of the Bundesliga campaign a week later.