The Germany international midfielder underwent the surgery this week to repair a persistent problem in his right ankle.
"The surgery went well," Hoeness said at Bayern's Annual General Meeting on Wednesday.
"We're optimistic that he won't be out for as long as first feared. At the moment it's looking better than we thought."
Bayern have not announced how long the 29-year-old will be out for, although reports in the German media claim that he could be sidelined for up to three months.