Thomas's four-under par effort gave him a 22-under total of 270 and a three-shot win over Japan's Matsuyama.
Thomas's four-under par effort gave him a 22-under total of 270 and a three-shot win over Japan's Matsuyama -- who arrived in Hawaii having won four of his prior five tournaments worldwide.
Thomas was, in fact, the only man to beat Matsuyama in that span, at the CIMB Classic in Malaysia in October.
But the 23-year-old American had to survive some tense moments on the back nine to again best Matsuyama, who started the day two behind Thomas and carded an three-under 70 for 273.
Former world number one and defending champion Jordan Spieth matched the best round of the tournament with a final-round 65, heading a trio sharing third on 276 alongside Pat Perez, who carded a 67, and Ryan Moore, who posted a 71.
It was a further stroke back to US Open champion Dustin Johnson, Patrick Reed and Brendan Steele.
Thomas was rolling with three birdies on the front nine. After a bogey at 10, and birdies at 11 and 13, he grabbed a five-stroke lead over Matsuyama at 22-under.
But Matsuyama narrowed the gap with a remarkable eagle at the par-four 14th, where his flop shot from 60 feet off the green found the hole.
Things got even more tense at 15, where Thomas hit out of the fairway into dense vegetation in a hazard en route to a double-bogey seven that sliced his lead to one stroke as Matsuyama parred the par-five from almost the same spot in the fairway.
Matsuyama had a 10-foot birdie putt to move into a tie for the lead at 16, but left it inches short.
And at 17 he three-putted for bogey as Thomas rolled in a three-footer for birdie to rebuild his lead before they both birdied Kapalua's par-five 18th.
"It's a great feeling," said Thomas, whose victory in the elite 32-man event for last season's title winners was his first tour title on US soil after his back-to-back CIMB Classic wins.
"I obviously stumbled a bit more than I would have liked on some of those holes, but I think it really shows where my game's at right now.
"I stuck it out to still get it done."
Spieth, who started the day in 19th, 10 shots off the pace, had eight birdies in his sparkling eight-under effort, including four in a row starting at the 12th.
"Very, very satisfying," he said. "To come back, fire a strong one today ... I certainly take a lot of confidence off this round going into next week."
World number one Jason Day, back in action this week after three months off rehabbing a troublesome back, had his ups and downs but finished on a high note with an eagle to cap his three-under 70. He finished tied for 13th on 279.
Although he said he always tees it up expecting to win, he said there were positives to take away.
"I didn't have anything in the back of my mind that my back was going to go out this week," he said. "The back held up."