Trahan's total of 268 bests Craig Bowden's total of 270 from last year.
'It's been a wild and crazy year for me, but I am really proud of the way I played today,' said Trahan. 'It was just one of those things where I was just able to go out and get things done.'
Watney, who owned the lead entering the final round, closed with an even-par 71 to take second place at 14-under-par 270. James Driscoll took third at 12-under-par 272 after a 68, while Chris Tidland finished one stroke further back at minus-11.
Trahan opened with a birdie at the first and moved to 12 under with a birdie at the par-5 fifth. The Clemson University graduate rolled in a birdie putt at the seventh.
He came right back to sink a 14-foot birdie putt at the eighth to briefly grab a share of the lead. Watney responded with a birdie on seven at Miccosukee Golf and Country Club to reclaim the lead.
Watney slipped back to minus-14 with a bogey at the 10th. Trahan grabbed the lead at 15 under with a birdie at the par-3 13th.
Trahan made it two in a row with a birdie at the 14th, which moved him two strokes clear of the field.
Watney got back within one shot of the lead with a birdie at the par-5 14th. However, he stumbled to bogey at the 16th to fall two back.
Trahan meanwhile parred his final four holes to close at 16 under. With the win, he jumped to No. 26 on the money list and gained entry into next week's Tour Championship and closes in on the top-20, which would earn him his PGA Tour card for next season.
'To play a bogey-free round on Sunday, you can't ask for anything more than that,' Trahan said. 'I've been hitting the ball well the last four or five weeks, but for me all year it has been a struggle to get the ball in the hole. I felt I had lost my ability to score. Finally, I had a good week last week with a top-10 and I just felt really good coming into this week.'
Watney missed birdie tries at both the 17th and 18th to come up short. However, he jumps from 36th to 19th on the money list.
'Hats off to D.J.,' said Watney. 'He played a great round and deserved to win. I am very disappointed right now because I felt I had my chances. But there are a lot of positives I'll take out of this week.'
Scott Gutschewski closed with a 3-under 68 to end at 10-under-par 274. He shared fifth place with Ryan Armour, Bryce Molder and Tim Wilkinson.