According to TVO television, the 31-year-old Germany international had left the city to visit his sick son and was involved in a minor road accident on Tuesday (March 31).
"Bayern defender Jerome Boateng left Munich yesterday without permission from the club," said the German champions in a statement on Wednesday.
"Boateng has transgressed the guidelines issued by the club by being too far away from his home.
"These guidelines govern the behaviour of the FC Bayern players in the current situation in line with government directives on restrictions on movement and the recommendations of the health authorities."
Bayern did not specify the amount of the fine, which was being donated to local hospitals.
"I know it was certainly a mistake not to inform the club of my journey, but at the time, I was only thinking about my son," Boateng told Bild newspaper.
"He was not in good health. If a son calls his father, then of course I will go, whatever the time of day."