Morikawa, who had been the pacesetter through the first two rounds, rallied from three strokes down with three holes remaining to force the playoff at Muirfield Village Golf Club.
He then stayed alive by draining a 24-foot birdie putt on the first playoff hole immediately after third-round leader Thomas had made a jaw-dropping 50-foot putt for birdie.
“Amazing,” said the 23-year-old Morikawa, who carded a final round 66 to finish on 19-under par 269 and won for the second time on the US PGA Tour.
Sunday’s win made up for a disappointing loss in another dramatic playoff finish at the Charles Schwab Challenge four weeks ago in the PGA’s return from the COVID-19 calendar shutdown.
World number five Thomas was trying to win for the 13th time on the Tour, but he was undone on the final hole of the playoff after his tee shot on the par-four 10th sailed right and landed behind a tree.
Thomas closed with a 69 but that included two bogeys in his final three holes after beginning his round with a two-stroke lead over Viktor Hovland, with Morikawa three adrift.
”I am pretty pissed off, it is the only way to explain it,” Thomas said. ”I had a three-shot lead with three to go and completely handed it over.
”Collin played great. He had a very tough hole at 17.
”We both made two great birdies on the first playoff hole. I had two chances to win this thing in regulation and on the second playoff hole and I didn’t get it done.”
This week’s Workday Charity Open is the first of back-to-back events at the Jack Nicklaus designed Dublin, Ohio course. The Nicklaus-hosted Memorial will follow next week.
After rain, wind and lightning led to two suspensions on Friday, organizers decided to move the tee times up on Sunday to avoid any more weather delays.
Morikawa started Sunday’s round three shots back after opening with a 65 and 66 to lead the first and second rounds.
He quickly fought his way back to the top of the leaderboard with two birdies and an eagle in his first five holes.
He made three more birdies on the back nine including the par four 17. Morikawa used an eight iron to spin his approach shot to eight feet then made the putt and celebrated with a fist pump.