Having started the day two behind, Matsuyama struggled on the front nine but closed the gap to one after a pitch in for eagle at the par-4 14th which was immediately followed by a double bogey seven at the par-5 15th from his opponent.
Both players parred the 16th but it was Thomas who applied the pressure when hitting first at the 17th, stuffing his approach within three feet of the hole.
Matsuyama played a decent second but, knowing he needed to make his 20 foot putt to stay in the hunt, ran his effort four feet past before missing the par attempt coming back.
It was the turning point of the tournament, the two shot swing to Thomas giving the American a big cushion with only the par-5 18th to play.
SHOTS LIKE THIS HELPED JUSTIN THOMAS TO VICTORY IN HAWAII:
"I stumbled more than I would have liked to do," Thomas said of his late mistake to let Matsuyama get close.
"But it shows where my game is at right now. I had some woes there, but I stuck it out to still get it done.”
For World Number One Jason Day the tournament was a positive one following an extended break from the game brought on by a recurring back injury late in 2016.
Day hadn’t played competitively since withdrawing from the Tour Championship in September but showed why he is the world’s top ranked golfer with a grandstand finish.
The 29-year-old made a spectacular eagle three at the 72nd hole to put the exclamation point on a 13-under par performance, good enough for T12.
“I think there was a lot of positives I need to take away from this week,” Day told Golf Channel after signing his card.
“I felt like other than today, for the most part of the week, I drove it pretty solid.
“I hit a lot of quality shots into the greens I just need to tighten it up a little bit with proximity.”
While his putting was not up to the standard of 2016 Day said he was pleased with his health and felt his back held up well to one of the most difficult walking courses on the Tour.
“The body felt great,” he said. “Obviously it is what it is but I didn’t have anything in the back of my mind that the back was going to go out this week.
“As you can tell it’s a pretty hilly walk and you get some awkward lies so the back held up great.
“I just have to stay diligent, keep being disciplined in what I eat and how I go about the process of trying to become stronger and if that works out then great, I’m healthy.”
Day was the best of the four Australians who teed up in the event, Rod Pampling next best at 11-under and T17, Aaron Baddeley finishing 6-under and T25 and Greg Chalmers 5-under and 28th.