Bruce Fleisher had set the original scoring mark in 2000 when he finished at 12-under-par 198. Thorpe finished just ahead of Bob Gilder, who ended at 14-under-par 196.
Thorpe, who matched the Champions Tour scoring mark of 60 on Saturday, got off to a rough start in the final round at Eisenhower Park's Red Course. He missed an eight-foot birdie try on the first.
Then at the par-4 fourth, he made a bad swing on a 3-iron and that led to a double bogey and dropped him one shot behind Gilder, who had birdied the third.
Thorpe birdied the seventh, as did Gilder. Thorpe grabbed a share of the lead at the next hole when he stuck a pitching-wedge within three feet for birdie.
'The big turnaround was at seven and eight for me,' said Thorpe, who takes home $225,000 for his sixth Champions Tour title. 'Especially after the double bogey at the fourth. That was a rude awakening and it put the pressure on.'
Gilder rolled home a birdie putt at the 11th to reclaim first place. Thorpe came right back with a two-putt birdie at the par-5 12th to tie the lead again. Gilder moved on top again with a birdie at the 14th.
However, it was all Thorpe down the stretch. He dropped a 7-iron within seven feet to setup birdie at the 16th. He sank that to join Gilder atop the leaderboard.
Thorpe stuck his third shot within 10 feet at the 17th and he rolled home that birdie putt to grab the lead. He capped the round with a two-putt par at the last.
He knew today would be a struggle after Saturday's outstanding round.
'One of the hardest things is to follow yesterday's round with another good round today,' said Thorpe, who picks up his first win since The Tradition in 2002. 'I knew Bob was a tough guy and he is a competitor.'
Gilder, who won the Emerald Coast Classic earlier this season, knew his rough start would come back to hunt him.
'I started out a little shaky,' said Gilder. 'After that, I seemed to make all the putts I needed, except the last one. Jim made some shots when he needed to and his birdie on 17 was big.
'I needed to have a shot at birdie on 17, but I didn't hit the shot I needed to and Jim made birdie there. I read the putt to go straight on 18, but I just missed it.'
Irishman Des Smyth continued his fine rookie campaign. He finished alone in third at 11-under-par 199. Mike McCullough ended one stroke further back at minus-10.
Jerry McGee had one of two aces on Sunday. He aced the 13th with a 3-iron for his 20th career hole-in-one. Rocky Thompson also had a hole-in-one, his came at the 16th. McGee finished in a tie for fifth along side Jose Maria Canizares, Rodger Davis and Mike Hill at 8-under-par 202.
Dave Barr, Vicente Fernandez, Gibby Gilbert, Tom Jenkins and Andy North shared ninth place at 7-under-par 203.