Teammates shielded Musiala as doctors rushed onto the field, and following brief treatment, he left the pitch looking dazed.
Musiala also collapsed in worrying fashion during Bayern's win over Leipzig on Saturday, but returned to action off the bench against Heidenheim.
"First things first – I’m doing well. I’m especially grateful for all your messages and your support," he said on social media.
"I understand that many of you are worried. Today, I’d like to put your minds at ease and explain the situation a little: I have been diagnosed with brief, temporary but readily treatable absences, which are caused by a neurological dysfunction.
"These can lead to the episodes that have occurred recently, such as against Leipzig and now in Heidenheim.
"I know that they may seem scary at first glance – but for me, they are currently part of my everyday life. I am receiving the best possible medical treatment for this and I am very optimistic. FC Bayern and the people close to me are always by my side and supporting me on this journey.
"The important thing is that there is no further health risk beyond this. In close consultation and regular communication with the specialists, it was my personal wish to face this challenge and, with the approval of the neurological specialists, to continue doing what helps me most in my recovery: simply getting on with my everyday life and continuing to pursue my passion of playing football.
"I have taken responsibility for that decision. Overall, I have a very good feeling and I’m on the right track. What helps me most on this journey is continuing to chase victories and titles with my team, with your fantastic support.
"I hope this helps you understand me a little better. At the same time, I ask for your understanding that I would like to continue keeping this matter within the circle of my closest confidants, the club and the experts."
The Bavarians won the match 4-2 in a dress rehearsal for the Franz Beckenbauer Supercup this Saturday against rivals Borussia Dortmund.