In a statement, Bayern said the 31-year-old had "transgressed the guidelines issued by the club by being too far away from his home."
"I know that it was certainly a mistake not to inform the club about my trip, but in the moment I only had my son in mind," Boateng told German newspaper Bild.
"He was not in good health. When a son calls his father, of course I will still go, no matter what time.
"For him I accept any punishment; after all, he is my son.
"I want to see the father who does not go in such a moment to be with his four-year-old son. If there is a punishment for it, then I respect it. I find it sad."
Bayern did not reveal the amount of the fine but said that they would be donating it to Munich hospitals.