However, the club's emergency doctor quickly signalled there was no cause for serious concern.
Musiala went down without any opponent contact in the 83rd minute at the Allianz Arena, just two minutes after scoring what proved to be the winning goal in a 3-1 victory, assisted by new signing Ismael Saibari. Team-mates immediately called for medical staff, and the emergency doctor rushed onto the pitch before giving the thumbs up moments later.
According to Sport1, Musiala had complained of dizziness and circulatory problems, with temperatures in the stadium reaching as high as 34 degrees during the match. Initial examinations by Bayern's medical team did not find anything of concern, though the 23-year-old is expected to rest for the next two days as a precaution.
Sporting director Max Eberl addressed the incident in the mixed zone afterwards.
"The most important thing is that he's doing well. There's nothing else to say about it," Eberl said.
Musiala was substituted around the 84th minute, having only entered the match as a substitute himself in the 66th minute. Luis Diaz and Nathaniel Brown scored Bayern's other goals, with Brajan Gruda replying for Leipzig, who fielded new head coach Martin Demichelis for the first time.
Bayern Munich also have fresh injury concerns over Konrad Laimer and Min-jae Kim, who both failed to finish the match with what appeared to be thigh problems.
Laimer went off early after taking a blow to the thigh and knee, replaced by Sacha Boey, while Kim was withdrawn after roughly an hour. The trio's fitness will now be closely monitored ahead of Bayern's Franz Beckenbauer Supercup meeting with Borussia Dortmund next weekend, with the club expected to give further updates on all three players in the coming days as their pre-season preparations continue.