Gwynn suffered the injury taking a swing in the sixth inning of the Padres' 5-1 victory at Wrigley Field over the Cubs.
The injury wasn't initially considered serious, manager Bud Black said, but Gwynn was given a more serious diagnosis after seeing a hand specialist late Wednesday.
Gwynn, who was officially placed on the 15-day disabled list Thursday, was flying back to San Diego to see a specialist there. Black wouldn't comment on the exact severity of the injury until the team hears from the specialist.
At any rate, Gwynn -- who according to Fangraphs has the second-best Ultimate Zone Rating in the National League among outfielders (13.6) -- likely won't be able to return this season given the Padres have 42 regular-season games remaining after Thursday.
Teammate Everth Cabrera suffered a similar injury to his left hand last season and was on the disabled list from April 20 until June 19.
"He's been great," Black said of Gwynn. "He's made some game-saving plays and made some plays with his arm. He's been extremely steady and sure-handed."
Gwynn has struggled this season offensively, hitting .212 in 327 at-bats. Chris Denorfia has received most of the playing time in center field in recent weeks, but the defense that Gwynn has provided has earned him playing time and rave reviews.
"Just in the time when I started playing more in left field, to have him there, knowing he was going to take care of me on balls was comforting," Padres outfielder Will Venable said. "His presence, the ground he covers ... that's a big loss. It's disappointing news."
Venable had a good idea something was wrong with Gwynn when he had to leave the game after a brief consultation near the dugout with trainer Todd Hutcheson and Black.
"Tony is not coming out of the game for anything. I knew it wasn't good," Venable said.
Black said the Padres could add an outfielder to the roster, though that might not happen until Tuesday when the team faces Arizona at PETCO Park.
Venable and Scott Hairston have experience in center field, though the way Denorfia has been playing, both players had seen more time in left field lately.