Thomas and fellow American Andrew Novak, who was seeking his first victory on the PGA Tour, both finished at 17-under 267 through 72 holes.
Novak was in the last pairing for the third time this season but couldn't find a way to win at Harbour Town Golf Links in Hilton Head Island.
Thomas, a two-time major champion, hadn't won since capturing the 2022 PGA Championship.
Thomas closed with a three-under-par 68 on Sunday, ending his bogey-free round with three consecutive pars.
Novak was off the mark on a would-be winning eight-foot birdie putt on the last hole of regulation and also had 68 for the round.
Thomas led after the first and second rounds. He went ahead on the 15th hole on Sunday with a third birdie of the day, but Novak countered from about 17 feet away on the 16th.
Daniel Berger (65), Brian Harman (69), Maverick McNealy (70) and Canada's Mackenzie Hughes (67) tied for third place at 14 under.
England's Tommy Fleetwood (70) was seventh at 13 under.
Defending champion Scottie Scheffler had climbed the leaderboard with three birdies in a five-hole stretch until a double-bogey 7 on the 15th hole and a bogey on No.17 doomed his round.
He shot 70, tying for eighth place with Russell Henley (70) and third-round leader Si Woo Kim of South Korea (74) at 12 under.
Kim was two over through 12 holes and his troubles continued with a double-bogey 5 on No.14.
After missing five straight cuts, Australian Cam Davis birdied three of his last six holes to tie for 13th at 10 under to pick up $US364,000 ($A570,000) at the $US20 million Signature event.
But Davis will curse dropping four shots in four holes mid round en route to a Sunday even-par 71. Â
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