Thompson closed with three straight rounds of 70 to post 2 under for the week, including a 6-foot par save on the final hole to remain two shots clear of Nicholas Thompson and Andrew Yun. Nicholas Thompson had a chance to tie with an eagle on the par-5 18th, but he failed to hole a wedge from 104 yards.
Kyle Thompson bounced back after playing the first six holes of the tournament in 6 over, and when the final round began he opened with four front-nine birdies. That helped him build a five-shot advantage before a double bogey on No. 16 created a bit of closing drama.
"I can't describe how well I played, especially the way I putted," Thompson said. "It's probably the best putting week of my life. I don't think I had a single three-putt. Just really grinded, made a lot of 6-8 footers. Didn't let the bad shots bother me and felt like I was in my own little bubble out there on the golf course."
Thompson, 37, finished 46th on the Web.com money list last year and last played a full season on the PGA Tour in 2012. It's the fifth Web.com Tour win of his career, and he becomes just the 11th player to win events on the developmental circuit in four different calendar years.
Players faced winds that blew from 20 to 40 mph throughout the week, and the 36-hole cut fell at 11 over which marked a new tour record. Former U.S. Amateur runner-up Corey Conners tied for fifth at 4 over, while PGA Tour veterans Sam Saunders (T-8), Chesson Hadley (T-11) and Erik Compton (T-17) were further off the pace.
This was the first of two Web.com events that will be played this month in the Bahamas and will feature a Sunday start and Wednesday finish.