Thomas holds nerve to edge former Masters winner Scott in Kuala Lumpur
The 22-year-old from Kentucky entered the final round tied for top spot with Brendan Steele, and surged clear on his own courtesy of a six-under 66 which included birdies at the 15th, 16th and 17th holes.
Thomas, who posted a course-record 61 on Friday to take the halfway lead, finished with a four-round total of 26 under par.
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Hide AdThomas - needing a par on the 18th - made things tricky for himself when he sent a 25-foot birdie putt five feet past the hole, but kept his cool to close out the triumph.
Asked how hard it had been to get over the line, he said: "It's a lot harder when you run 20-footers about five feet past the hole.
"It's tough to win. (But) look at guys like Rickie (Fowler). He's done pretty well for himself and it took him a while to win too.
"I understand we're in a sport where your winning percentage isn't in your favour. I've put myself there a bunch. I just need to keep doing so, and moments like this can happen."
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Hide AdThe success lifted the University of Alabama graduate to No 1 in the fledgling 2015-16 FedExCup standings, three events into the campaign.
Former Masters champion Scott burst into contention with a flawless final round of 63 which included seven birdies and an eagle, but fell just short.
Steele (68) had to settle for a share of third place alongside fellow American Kevin Na (67).