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.
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)
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