Van Pelt shot a 4-under-par 68 Sunday for a 72-hole total of 16-under 272. Dufner, who started the day one stroke back of Van Pelt, turned in a 3-under 69 in the final round and ended up at 14-under for the tournament.
Alejandro Canizares also shot a final-round 68 and wound up third at 11-under while Michael Hendry, with a 69 Sunday, was fourth at 9-under 279.
A first-hole birdie allowed Van Pelt to grow his third-round lead to two strokes over Dufner. They matched birdies at the third and seventh holes, with Dufner chipping in at No. 7 for the second straight day.
Dufner had a bogey at No. 8 and got back within two strokes with a ninth-hole birdie.
Both players had birdies at 10 but Van Pelt added another at the 11th to go up by three. Dufner pulled close with a tap-in birdie at 14, where Van Pelt had a three-putt bogey. However, Van Pelt dropped a short birdie putt at 15 for the final margin.
It was Van Pelt's fourth professional win overall. He won the U.S. Bank Championship in Milwaukee for a PGA Tour victory in 2009 and took an Asian Tour win in Malaysia a year ago. Van Pelt also won on the Nationwide Tour in 2003.