Musiala scored Bayern's third goal before appearing to struggle in the heat and suddenly staggering to the ground in the closing stages. Medical staff immediately attended to the 23-year-old, while teammates rushed over to check on him.
He was eventually able to walk off the pitch without assistance, although he appeared dazed as he made his way into the tunnel.
Bayern sporting director Max Eberl later moved to ease concerns over the incident, saying: "The most important thing is that he's doing well."
Reports in Germany indicate Musiala suffered dizziness and circulation problems while playing in temperatures of around 33 degrees Celsius. Preliminary checks have reportedly suggested that there is no serious concern and that he could return to full training within a few days.
That would mean Musiala is likely to sit out Bayern's final friendly against FC Heidenheim on Wednesday before targeting a return for the DFL Supercup against Borussia Dortmund at the end of the week.
The incident overshadowed an otherwise encouraging afternoon for Bayern, who continued their strong pre-season with goals from Nathaniel Brown, Musiala and new signing Luis Diaz. Konrad Laimer also had to leave the match early after picking up a knock.
Musiala's fitness is particularly important to Bayern after the attacking midfielder endured a difficult period following his serious leg injury at last summer's Club World Cup. He also underwent planned surgery to remove a metal plate from his leg during the current off-season.