The 22-year-old from Kentucky, in his second year on Tour after a solid rookie season, was tied with compatriot Brendan Steele for the lead coming into the final round.
Thomas mixed an eagle, six birdies and a double bogey on the 14th for a six-under-par 66 that took him to a total of 26-under in the $7 million co-sanctioned Asian Tour event, the third of the new PGA Tour season.
Scott scorched the Kuala Lumpur Golf and Country Club and climbed up the leaderboard with a round of nine-under-par 63, that included seven birdies and an eagle on the par-five third.
Thomas needed a par on the par-five 18th to avoid a playoff with Australian Scott but put himself under pressure when his 25-foot birdie putt went five feet past the hole.
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But he made no mistake this time and holed the putt for his maiden win.
"It's tough to win," Thomas said after completing his final round. "I understand we're in a sport where the winning percentage isn't in your favour.
"I've put myself in positions to win, and I just need to continue to do so."
Steele, the other overnight leader, carded a 68 to finish tied for the third spot with South Korean-born American Kevin Na on 24-under.
(Writing by Sudipto Ganguly in Mumbai; editing by Amlan Chakraborty)
