The 26-year-old American birdied the third extra hole to beat Reed after defending champion Schauffele had been eliminated with a three-putt par on the first playoff green.
World number four Thomas stuck his third shot three feet from the pin at the par-five 18th on the Plantation Course in Kapalua, Hawaii, to set up an easy birdie and watched as Reed missed his seven-foot putt to extend the playoff.
All three had finished 72 holes with 14-under par totals of 278 after Thomas, who enjoyed a two-shot lead with three to play, bogeyed two of the last three holes.
He fell back to 15-under at the 16th before his three-wood second shot at 18 found the thigh-high grass in a penalty area on his way to a bogey in a four-under-par final round of 69.
Playing partner Schauffele, the world number eight, reached the green in two, but missed a seven-foot birdie putt for victory, carding a three-under par 70.
Reed, ranked 11, was already in the clubhouse on 14-under after capping a bogey-free seven-under 66 with a 20-foot birdie putt at the 72nd hole.
Reed, the 2018 US Masters champion, had putts to win on each of the first two playoff holes but was unable to get efforts from 30 feet and 12 feet to drop.
“For some reason I was supposed to win this week,” Thomas said. “I got very, very lucky to have that putt.
“But I also stuck to my process,” said Thomas, who like the entire field in the winners-only event dealt with challenging, gusty winds for a fourth straight day.
“I truly felt like through 15 holes it was one of the best rounds I ever played,” said Thomas who started the day one stroke off Schauffele's lead and pulled level with a birdie at the eighth where Schauffele bogeyed.
Disaster at 18
He kept the accelerator down with birdies at nine, 10 and 11, and added two more at 14 and 15 - where his putt through the fringe circled the cup before rattling in.
“I was in such control tee to green, I was putting it beautifully, my irons were awesome,” Thomas said. “I hit a really good drive on 16, just the wind took it more.
“Eighteen," he admitted,” was just a disaster.
“But it worked out, so I guess I can't complain,” Thomas concluded.
Schauffele said Thomas's run of six birdies in eight holes was astonishing, especially given the windy conditions.
“He was hitting ridiculous shots, making good putts in the wind, and he deserved the lead he got,” said Schauffele.
But he was disappointed that he didn't take advantage of his own opportunity.
“I should have won the tournament,” Schauffele said.
“I mean, JT was right there, but with the circumstances given I should have closed it up and I didn't.”