Thomas, the third-round co-leader, erased a two-shot deficit over the final nine holes by shooting a 5-under-par 66 to beat runner-up Spieth by three strokes for his PGA Tour-leading fifth win of the season.
The PGA champion finished at 17-under 267 over the par-71, 7,342-yard layout at TPC Boston. Yet it was Thomas' ability to remain steady down the stretch that was the decisive factor in the second of four FedExCup Playoff events.
Thomas bogeyed No. 11 but closed with a pair of birdies and five pars to pull away as Spieth and third-round co-leader Leishman stumbled badly over the final nine holes.
"Yeah, it was a good day. It was a patient day," said Thomas, who also praised caddie Jimmy Johnson after the victory that cemented his front-runner status as PGA Tour Player of the Year.
"It just was a great week because I felt like I didn't have my best stuff at the start of the week and that's just something I've gotten so much better at, and I'm proud of myself more than anything," Thomas said. "It was a great win for Jimmy and myself both, for sure."
British Open champion Spieth and Leishman were two shots clear of Thomas with nine holes to play after each burned up the front nine with 30s.
Spieth then had a bogey at the 12th with a birdie at No. 13, and he bogeyed Nos. 14 and 18 to allow Thomas to blow past him. That derailed a "dream start" by Spieth, who had three birdies and an eagle over the first four holes.
"I've been striking the ball well. I didn't think anything was going wrong," Spieth said. "I got unlucky on 12, and from there, the one on 14 was just a bad swing, and that one really hurt. I brought it back on 13. Fourteen was the difference-maker for me. That one was a tough one because I really did a good job."
Leishman saw the lead evaporate with five bogeys on the back side, including three straight from Nos. 10-12. Like Spieth, it was a stunning turn after the Australian ripped off six birdies on the front nine. His final-round 70 left him alone in third at 271.
"You know, it was obviously a disappointing back nine for me," Leishman said. "You know, got things going just the way I wanted to on the front and then a bad tee shot on 10. There was some tough holes out there, but certainly not 10 shots tougher than the front nine."
The 47-year-old Mickelson birdied three of the first four holes, but a double bogey at the par-4 14th quelled his momentum en route to a 68. He is optimistic his four consecutive sub-70 rounds will earn him a spot on the U.S. Presidents Cup team.
"We'll see. I hope so," said Mickelson. "But more than that, I don't feel like it was a one-way thing. I think that this is a big step for me as far as getting back to where I want, shooting the scores, playing, having energy, being able to practice, all these things. It was a good start."
World No. 1 Dustin Johnson stumbled to a 73 and finished in a tie for 18th at 277.