A statement from the German champions said that the Brazil international had an operation to remove "loose joint fragments", but he is expected to begin his recovery programme in two weeks.
There is a chance that the Bundesliga season could resume towards the start of May despite the ongoing coronavirus pandemic which has halted the majority of football across the globe.
Coutinho has been in impressive form for Bayern this season, scoring nine times and contributing eight assists in 32 appearances in all competitions, having arrived on loan from Barca last summer.
"On Friday, Philippe Coutinho underwent an operation on his right ankle, during which loose joint fragments were removed," read a club statement. "The operation was a success. The Brazilian will begin his recovery programme in around 14 days."