"Once in a while the hole gets in the way," Van Pelt joked.
His eight-iron approach had finished on a back tier of the green and he was looking at a possible three-putt.
"Lo and behold the ball goes in," said the world number 24.
Van Pelt closed with a 67 to finish on 12-under 204, one-shot clear of fellow American Jason Dufner (67) and two ahead of 20-year-old Emiliano Grillo of Argentina.
Three shots further back is Britain's David Howell, who is trying to get back into the winners' circle after spending years battle injury. Howell is on -7, alongside Spain's Alejandro Canizares.
Grillo, seeking his first win as a professional, battled bravely for his 73.
Van Pelt, paired with Grillo, said the youngster should not be disheartened.
"He played really well and must have had five or six putts which hung on the edge today. There is plenty more upside for him (Grillo) to take out of the round," the American said.
After a composed front nine, the Argentinian had four bogeys on the back to come home in 39.
"I don't know what happened on the back nine. I had four bogeys and they were all pretty much good shots," Grillo said.
He remained upbeat about his chances.
"I have a good chance tomorrow. I'm playing in the group in front of the last group out. All the crowd will be with them (Dufner and Van Pelt) and they are going to have the pressure."
Grillo had an outstanding amateur career and played senior golf for his country when he was 14 years of age.
Van Pelt said the key to his score had been the four par fives at Lake Karrinyup which he has played them in 10 under par.
"That's where you have to make your score around this golf course," he said.
US Ryder Cup player Dufner said he felt very comfortable going into the final day after setting up his round with an eagle at the third and a chip-in for birdie on the seventh.
"I hit it stone dead at nine then made birdie at 10, 11 and 12. You have to make your score around here from seven to 15. It's a very tough finish," Dufner said.