Fowler fell two shots off the lead when he bogeyed the 14th hole of the final round, but responded with birdies at the 15th, 16th and 18th to finish 12 under par and snatch victory from Ryder Cup team-mate Matt Kuchar.
That brought back memories of the 26-year-old’s victory in the Players Championship at Sawgrass in May, when he played the last six holes in six under par, taking a tournament-record 11 shots to finish birdie-eagle-birdie-birdie.
Fowler then defeated Kevin Kisner and Sergio Garcia in a play-off, just days after he and Ian Poulter were voted the most overrated players by their peers in an anonymous survey conducted by Sports Illustrated.
Kuchar had set the clubhouse target on 11 under par after a closing 68, finally ending the hopes of Scotland’s Marc Warren who had finished 10 under par four hours earlier after a superb 64.
Fowler had dropped his second shot of the day after driving into a fairway bunker on the 14th, but holed from nine feet on the next, two-putted the par-five 16th and then hit a superb approach to two feet on the last.
That left France’s Raphael Jacquelin needing to hole his second shot to the 18th to force a play-off and his approach span back to within inches of the hole, but Fowler was not to be denied.
Fowler will now hope to emulate the last American to win the Scottish Open, Phil Mickelson tasting victory at Castle Stuart in 2013 before going on to win the Open at Muirfield.
“It’s pretty special,” Fowler told Sky Sports 4. “I played great coming in and it’s been a great week. I will have a bit of time tonight to let it sink in and get right back at it next week.
“This is a big win. I had a couple of missed cuts after winning the Players, which was disappointing, so it feels good to get back on form.
“I had to dig deep. I was a little bummed to drop a shot on 14 but knew I had some birdie holes coming in. I had played the last four holes well this week and luckily 14 didn’t cost me.”
Fowler, who finished in the top five in all four majors last year, added: “There are a few things we can tighten up for next week but I am looking forward to getting back to St Andrews, the Home of Golf, and getting into contention.”
Jacquelin had the consolation of securing a place in the Open with his share of second place, with overnight leader Daniel Brooks – who carded a closing 73 – and Sweden’s Rikard Karlberg claiming the other two spots.