Thomas finished off a shot from Lee Westwood, but was in danger of losing the cut Friday before carding two birdies into the final three holes to stay in contention.
It was followed by a 64 on Saturday and a final round featuring three little birds and an eagle between the ninth and twelfth holes as it advanced ahead of Westwood.
After his victory, Thomas recalled how his grandfather, who died last month at the age of 89, was at the forefront of his mind as he sealed the victory.
Westwood and Bryson DeChambeau, another player who claimed victory on Sunday, retired the nine forwards from the remarkably difficult TPC Sawgrass course.
Thomas, who took home $ 2.7 million in prizes, now has 14 wins on the PGA Tour.
He is only the fourth player to win a major one, the 2017 USPGA Championship, the FedEx Cup, a Golf World Championship and the Players Championship.
“It reproduced a lot of what he was saying in my head,” Thomas said.
“He likes to give me a lot of pity, especially when he’s not here … we’re all pulling for him and I’m very happy to know that everything has gone well for him.
“Part of me wish I was here so I could rub his face a little more, but I’m happy and I hope he’s happy and I appreciate his help.”
DeChambeau and Brian Harman finished tied for third place at 12 behind Thomas and Westwood, while Talor Gooch and Paul Casey shared fifth place at 11 below.