Craig Lile, who carded a 12-under 60 on Friday, finished alone in second place at 24-under-par 264. Tjaart van der Walt, one of two overnight co-leaders, carded a 5-under 67 to come in third at minus-23. Steve Ford and Todd Demsey both climbed from a tie for 12th to a share of fourth with matching rounds of 5-under 67. They finished the event at 22-under-par 266.
Van Pelt closed his round at The Champions Club with a bogey on Saturday, but that was his last of the tournament. He rolled in a seven-foot birdie putt at the par-4 fourth. The Oklahoma State alum then eagled the par-5 sixth to climb to 19-under for the event.
He really caught fire around the turn. Van Pelt birdied the ninth from six feet before draining his second eagle of the day at the 10th. He was not done either.
Van Pelt converted back-to-back birdies from the 11th, from 65 feet and 35 feet respectively, to complete a four-hole stretch at 5 under.
With a chance at 59 staring him right in the face, Van Pelt settled down and missed a shot at history. He parred the 13th but responded with a birdie at the next.
Van Pelt then parred the 15th and the 16th but two-putted for birdie at the 17th to get to 26 under.
'They asked me how this felt and I said it was more a sense of relief to get the first win,' said Van Pelt, who earns $99,000 for the victory. 'I've had a couple of chances before to win but for whatever reason couldn't get the job done.'
The win moves Van Pelt to fourth on the money list with $201,729 and nearly assures him of gaining his PGA Tour card for next season.
'Winning and knowing I'll be on the PGA Tour again next year helps me out a lot and will free me up,' said Van Pelt, who was celebrating his fourth wedding anniversary on Sunday. 'The fact that I've been out there a couple of times and not done as well as I had hoped, gives me motivation to get back out there as soon as possible.'
Lile needed to birdie the 18th to force a playoff with Van Pelt, but instead he stumbled to a bogey. Lile came firing up of the gates and it looked as though he would match the 60 he shot earlier in the week.
The South African birdied five of his first six holes and eight of his first 11 to move to 25 under for the event. However, he bogeyed the par-3 12th to fall out of the lead. He reclaimed that stroke with a birdie at the 15th, but his late bogey cost him a chance at a playoff.
'If you're not going to win then second place isn't so bad,' said Lile. 'Van Pelt's round was really, really good. I went out this morning and thought if I could shoot 65 then somebody would have to go out and beat me and Bo did just that.'
Blaine McCallister fired an 8-under 64 Sunday to move into a share of sixth place with Ted Purdy and Roland Thatcher at 21-under-par 267.
Long-hitting Victor Schwamkrug carded three rounds of 7-under 65 but his 1-over 73 in the second round hurt his chances for a victory. He finished the event at 20-under-par 268.
Jay Delsing, the 2002 champion, struggled to a 73 Sunday. He finished at 8-under-par 280 in a tie for 63rd.