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 50-foot bomb.
The 23-year-old Morikawa finished the week at 19-under par 269 to win for the second time on the US PGA Tour.
Sunday’s win also makes up for a disappointing loss in another dramatic playoff finish at the Charles Schwab Challenge four weeks ago.
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 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.
This week’s Workday Charity Open is the first of back-to-back events at the Jack Nicklaus designed Dublin, Ohio course, added in to boost the coronavirus-disrupted calendar.
The Nicklaus-hosted Memorial will follow next week.
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