The England international suffered a broken fibula when he fell awkwardly under Karl Henry's challenge during the game at Craven Cottage.
The 29-year-old was given oxygen on the pitch and was stretchered off before being taken to hospital and manager Mark Hughes admitted it could be at least January until Zamora is back in the fold.
However, news that ligament damage was also discovered during the operation could mean that the striker could still be ruled out for up to four months with the club refusing to give a timescale on when he might return.
Zamora, who scored 19 goals for Fulham last season signed a new four-year contract last Friday.
A statement on the club's official website read: "This morning, Bobby Zamora underwent an operation on the injury sustained in Saturday's match against Wolverhampton Wanderers.
"The operation was views as successful by the surgeon and the fracture to the fibula was repaired, ligament damage was also discovered and repaired during the operation."