Thomas went first, making a 50-foot downhill putt for what appeared to be the victory. But Morikawa wasn't going anywhere. He stayed alive by draining his putt, from just inside 25 feet, to send it back to the 18th tee for a second playoff hole.
Morikawa sealed the win on the 75th hole, two putting on the green after Thomas missed the fairway off the tee and had to chip out from behind a small tree with his second shot.
The win was Morikawa's second in just his 24th start as a pro.
"This is a huge kind of stepping-stone," Morikawa said. "We got number one (win) out of the way, we got number two - let the gates just open and let's keep going because obviously it was a tough loss at Colonial a month ago, but I learned a lot.
"This is just more positives, more learning for me."
Leading final-round scores on Sunday in the PGA Tour Workday Charity Open at Muirfield Village in Dublin, Ohio (x-wins at 3rd playoff hole, USA unless noted, par-72):
269 - x-Collin Morikawa 65-66-72-66, Justin Thomas 68-66-66-69,
273 - Viktor Hovland (NOR) 69-67-66-71
274 - Chase Seiffert 68-69-70-67
276 - Gary Woodland 73-68-66-69, Ian Poulter (ENG) 68-69-69-70
277 - Billy Horschel 72-69-70-66, Russell Henley 70-70-70-67, Patrick Cantlay 70-72-70-65, Sam Ryder (USA) 70-72-66-69, Charley Hoffman 74-68-68-67, Kevin Streelman 70-64-71-72, Jason Day (AUS) 69-71-70-67
278 - Matt Jones (AUS) 69-72-67-70, Sepp Straka (AUT) 69-70-69-70, Xander Schauffele 69-73-66-70
279 - Stewart Cink 72-69-68-70, Sam Burns 69-66-70-74, Chez Reavie 70-72-70-67, Talor Gooch 71-68-71-69, Rory Sabbatini (SVK) 69-68-69-73