Cantlay trailed by four strokes before he carded birdies on four of five holes on the back nine to take control on Sunday at Sherwood Country Club. He fired a 7-under par 65 in the final round.
"It's really great to win at home," Cantlay, a Long Beach, Calif., native told reporters. "I look forward to hopefully winning at Riviera. Anytime you win close to home it just feels a little sweeter.
"I felt comfortable all week. I like this cloudy California weather. I'm used to it and it's what I grew up with. It was just a nice week."
The victory was Cantlay's first on the PGA Tour since the 2019 Memorial Tournament.
Cantlay was 23-under through four rounds. He moved from No. 14 to No. 9 in the Official World Golf Ranking due to the victory. He also moved up to No. 2 in the FedEx Cup standings.
Thomas fired a 3-under par 69 and Rahm shot a 4-under par 68 over the final 18 holes. Rahm missed a chance to take over the No. 1 spot in the Official World Golf Ranking with his second-place finish.
Russell Henley, Cameron Smith, Bubba Watson and Ryan Palmer tied for fourth place. Corey Conners, Joel Dahmen and Cameron Champ tied for eighth place. World No. 4 Collin Morikawa tied for 50th. No. 5 Rory McIlroy tied for 17th.
Tiger Woods tied for 72nd at 1-under par for the tournament.
"I played the par 5s awful," Woods said. "This is a golf course where you have to take advantage of the par 5s, because they all are reachable.
"The only thing I can take out of the week I did positive is that I putted well."
Cantlay, 28, made five birdies and a bogey on the front nine in Sunday's final round. He birdied Nos. 11, 13, 14 and 15 before he made a bogey on No. 16 and carded pars on his final two holes to win the tournament.
Sebastian Munoz shot a 64 for the first-round lead at the Zozo Championship. Thomas took over the second-round lead at 14-under par before he held a one-stroke lead on Rahm entering Sunday's final round.
The Bermuda Championship is the next tournament on the 2020-2021 PGA Tour schedule. That tournament runs from Thursday through Sunday at Port Royal Golf Course in Southampton, Bermuda.
Golfers will participate in the Vivint Houston Open from Nov. 5 to 8 before the 2020 Masters Tournament from Nov. 12 to 15 at Augusta National Golf Club.