Gwynn, who suffered the injury on Wednesday on a swing against the Cubs, returned to San Diego on Thursday and saw a specialist, who confirmed what the hand specialist in Chicago saw -- a broken hook of the hamate bone.
The surgery was performed Friday afternoon at Scripps Clinic.
Gwynn is expected to miss the rest of the regular season.
San Diego shortstop Everth Cabrera suffered a similar injury, to his left hand, a year ago. Cabrera returned two months later, though he was playing in a Minor League rehabilitation assignment sooner.
"He's disappointed but realistic," Padres manager Bud Black said of the conversation he had with Gwynn. "He knows what's ahead of him."
Gwynn, who was hitting .212 with 17 stolen bases, was one of the top defensive players at his position in the National League.
"It's a loss. It's a loss for the team," Black said.
Black said he was unaware of any specific timetable for Gwynn's recovery, though he might have a better answer in "two to three weeks."