Flanagan, the 2003 US Amateur Champion, had also won this event during his stunning season on the Nationwide Tour in 2007 where in winning three times, he advanced to the PGA Tour.
Things have been a struggle since for the still only 27 year old but the talent and the confidence he displayed at the US Amateur and in his stellar season in 2007 appears to be returning.
Flanagan recently Monday qualified for the Wells Fargo Championship and although he struggled it suggested his game was on the way back.
Today he birdied three of his last four holes to force the playoff after what had been a great putting display.
Percy agonisingly bogeyed his final hole to Flanagan to open the door for Flanagan although the winner can consider himself very lucky after his approach to the 72nd hole hit the grandstand behind the green and bounced back to 15 feet.
Flanagan converted for the birdie to tie with Percy who had finished ten minutes earlier.
Both bogeyed the first extra hole, then parred the second before Percy took double bogey at the 3rd and Flanagan sealed the victory with a great up and down from the greenside bunker.
The victory was worth US$108,000 and Flanagan moves to 11th on the money list and Percy advancing on his 19th position to now be 6th.
Alistair Presnell and Scott Gardiner tied for 8th, Gardiner's final round of 64 the best of the day.
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