Having snatched the lead with a 60 foot putt on the final green at the end of the third round, the 37 year old was never caught on the last day.
A four under par 68 gave Van Pelt a 16 under total and left him two clear of Dufner, with first round leader Alejandro CaÃƒÂ±izares of Spain coming through to take third on 11 under.
"Jason and I had a great battle and played well," said Van Pelt. "It definitely got tight there at the end but luckily for me I came out on top.
"I have a lot of respect for Jason and his game - he's a world class player and I knew it was going to be tough today. I knew he was going to keep the pressure on me, and I needed to play well if I was going to come out on top.
"It was fun. That's why you practice - to give yourself a chance to win with nine holes to go.
"All in all I was pleased with how I played today. I had a loose shot there on 17 that I was not that happy with, but fortunately I had a lead at that point and was able to make a putt on 18 and get it done.
"Lake Karrinyup was a great test of golf all week. It's been a battle; the wind blew, the greens were firm and fast, and it was just a joy to play all week.
"Whenever you get a lead you want to take advantage of it so it was nice to finish one off this week."
New Zealander Michael Hendry extended his lead on the PGA Tour of Australasia's Order of Merit when he finished as the leading Australasian in 4th position.
Greg Chalmers was 10th and Steve Jones earned a nice cheque when despite a costly double bogey at his final hole he finished 11th.