For much of the day, Fowler struggled to find his rhythm in the strong winds and cold temperatures at Gullane Golf Club, but rose magnificently to the occasion late on with three birdies in his final four holes "“ including a tap-in at the last courtesy of a wonderful wedge shot.
A round of 68 for a 12 under par aggregate total saw him leapfrog compatriot Matt Kuchar, who had previously set the clubhouse target on 11 under par after he too signed for a 68.
RaphaÃƒÂ«l Jacquelin, playing alongside overnight leader Daniel Brooks in the last group, needed an eagle on the 72nd hole to force a play-off, and the Frenchman almost pulled off the unlikely feat when his approach stopped within a foot of the cup.
That tap-in birdie set the seal on a level par round of 70, and his tied runner-up finish with Kuchar earned Jacquelin a place in next week's Open Championship.
Brooks struggled in a round of 73, but the Englishman took ample consolation from a place at St Andrews along with Sweden's Rickard Karlberg, who closed with a superb 64 to claim the third and final Open Championship berth.
Karlberg's score was matched by Marc Warren, who finished as the leading home player on ten under par.
"I felt really good coming down the stretch," said Fowler. "It was nice to be back in contention again, and I'm excited about where the game is at. I have a few things we need to straighten out before Thursday, but I'm very excited about next week now.
"Probably the only thing that would be more special than this would be winning next week. But winning on a links golf course in Scotland, the Home of Golf, is a special week. I beat some pretty good players out there today. The guys were on top of their games. I didn't see many scores being under par with the way the wind was blowing, so it was going to be a tough test of golf. I'm definitely proud of how I finished."
Fowler is likely move as high as 5th in the world ranking as a result of his win.
John Senden closed with a round of 67 to finish in 22nd position to be the leading Australian and the only one to make the cut.
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