Thelen had previously won the 2000 PGA CPC crown.
'It's awesome,' Thelen said. 'When I got the trophy (The Walter Hagen Cup), I got goose bumps. You're champion again for another year. And people earn their way to get here, all 156 players.'
Thelen trailed overnight leader Steve Schneiter by one stroke entering the final round at Twin Warriors Golf Club. Thelen took control quickly, earning an eagle on the par-5 first to climb to 5-under.
Schneiter, 1995 PGA CPC Champion, fell three shots off the pace with a double- bogey at the second. His slide continued as he carded back-to-back bogeys from the third that dropped him back to even-par for the championship.
Thelen moved to minus-6 with a birdie at the par-4 fifth. He bogeyed the seventh while Schneiter birdied the same hole to cut the deficit to four shots. Schneiter continued to cut into the lead as he birdied the next three holes for four straight birdies.
Now trailing by one shot, Schneiter struggled to a bogey at the 11th. Both men would then birdie Nos. 12 and 13. With those birdies, Thelen moved to 7- under while Schneiter stood at minus-5.
The two men each ran off four straight pars to head to the 72nd hole. Schneiter saved his par, but Thelen made things interesting. He bogeyed the last hole to drop to minus-6, but the crown and the $53,000 pay check were his.
'I had a two-shot lead coming into the last hole and I thought I hit an absolutely perfect drive,' Thelen said. 'But it hit a little right where it's supposed to kick left and hit a rake and was buried. I tried to get it out into the fairway, where I'd have a sand wedge in. That was a mistake, I should have laid it back further.
'The sand wedge was probably one of the worst shots I've hit all week. Then I responded with a great bunker shot. I'm glad I did, because Steve hit a great putt.'
'It was ugly, it was bad,' said Schneiter. 'But, I was proud of the way that I fought back and finished. I tried to keep to my game plan and I knew I needed to make birdies. I knew that Tim wouldn't do anything stupid. He's a good player and steady. I was proud that I could come back.'
Thelen and Schneiter, along with the rest of the top-25, all qualified for the 85th PGA Championship, which is set for August 14-17 at Oak Hill Country Club in Rochester, NY.
Kevin Burton, Dino Lucchesi, Ron A. Philo, Jr. and Bob Sowards shared third place at 1-under-par 287. Terry Hatch and Alan Morin were one stroke farther back at even-par 288.
Don Berry, Sean Farren, Jeffrey Lankford and Mike Schuchart tied for ninth at 3-over-par 291. Michael Combs, Wayne DeFrancesco, Ken Schall and Rick Schuller were one shot behind them at plus-4.
Tim Fleming, John Guyton, Scott A. Porter and Chip Sullivan came in at 5-over-par 293 in a share for 17th, while J.C. Anderson, Rob Labritz, Cary Sciorra, Dave Spengler and Dave Tentis all finished at plus-6 and were the final players to qualify for the PGA Championship.
Barry Evans, the 2002 PGA Club Professional Championship winner, missed the cut by one shot after rounds of 74 and 77.