With the win, Morikawa earned his second PGA Tour title in only his 24th pro start. It was a remarkable turnaround for the 23-year-old rising star, who missed the first cut of his career two weeks ago at the Travelers Championship.
"This is a huge kind of stepping stone," Morikawa said. "We got No. 1 out of the way. We got No. 2. Let the gates just open and let's keep going."
Morikawa forced the playoff by making up three shots with three left to play. He had two pars and a birdie at the end of the back nine, but Thomas bogeyed two of his final three holes.
Thomas was ultimately done in by an errant tee shot on hole No. 10 in the third round of the playoff. The misfire ended up in the rough behind a tree, forcing him to pitch out 102 yards short of the green.
Thomas missed his 15-foot par putt, leading to Morikawa's 2-putt par and the victory. Both ended regulation at 19-under 269.
"It's completely unacceptable to give up a 3-shot lead with three to go," Thomas said. "I'm upset, I'm disappointed in myself. But at the end of the day it's over with now, and I just need to take some time this afternoon and tonight to build on it and figure out what I can do better going into next week."
Norway's Viktor Hovland posted a 71 and finished alone in third. American Chase Seiffert shot a final-round 67 and came in fourth, while Gary Woodland and Ian Poulter tied for fifth at 12-under 276.
Brooks Koepka, Jordan Spieth, Bubba Watson, Justin Rose and Jim Furyk were among the players who failed to make the cut Saturday after some of Friday's second round was moved back a day because of inclement weather.
The PGA Tour returns Thursday for the opening round of the Memorial Tournament at Muirfield Village in Ohio.