The 32-year-old American's 23-under total of 265 left him one stroke clear of compatriots Billy Horschel (67) Richy Werenski (66) and Tom Lovelady (68).
Merritt, whose only previous win on the PGA Tour came at the 2015 Quicken Loans National, was one of eight golfers who did not play on Sunday when rain and thunderstorms interrupted the final round before play was called off for the day.
For Merritt, who led or shared the lead after each round and tied the course record with an opening 62, the highlight of his final round came when he holed out from 133 yards to make eagle at the par-four eighth hole.
The victory earns him a two-year exemption on tour as well as a spot in the Aug. 9-12 PGA Championship at Bellerive Golf Course in St. Louis.
"We're gonna celebrate this one for a while and enjoy the fact we've got two more years out here," Merritt told Golf Channel.
"It's been a few years. I'm sure I'll have some emotions here the next 10 minutes. It's been a struggle, not just for myself but for my family, always cheering me on."
(Reporting by Frank Pingue in Toronto; editing by Ken Ferris)
