Fitzpatrick won 135-115 after making use of the double points on offer for the final shot to overhaul the American and win the exhilarating event ahead of the Aberdeen Standard Investments Scottish Open.
The Englishman prevailed in the innovative quickfire format that also included Major Champions Graeme McDowell and Justin Thomas and European Tour winner Lucas Bjerregaard and Tyrrell Hatton.
Kuchar appeared on course for another Hero Challenge success when he opened the final by hitting the bullseye for 50 points with his first of six shots on the 15th hole.
He stretched his lead to 80-50 after Fitzpatrick failed to score on his third attempt, but the Englishman fought back and was just 95-85 down ahead of the final shot.
With double points on offer, Fitzpatrick hit the 25-point zone for a score of 50, while Kuchar landed in the 10 for a 20-point haul.
“It was good fun out there, I had to do it the hard way.” said Fitzpatrick. “It was great to get the win, it suits me having to hit low shots.
“Matt is a great player, obviously he won the Hero Challenge last year, but he’s a proper golfer. The whole evening was really good fun. It was nice go out there on a Tuesday night and get the crowd fired up for the week ahead.
“My caddie and I walked the course this afternoon when the weather wasn’t too good, so to see so many people out there supporting us was great.”
Both finalists had to come through a tie-breaker in their respective semi-finals.
With both games ending level after all players had taken six shots, the finalists were decided by nearest to the pin.
Fitzpatrick overcame Graeme McDowell when he shot to within three feet, while Kuchar levelled his clash with Bjerregaard with his final effort before winning the tie-breaker following an official measurement.
Fitzpatrick earlier came through a group containing Bjerregaard and Thomas, top-scoring with 160 from his 10 shots in 90 seconds.
Kuchar had the highest score of the first stage as his 195 saw him win the second group, with McDowell edging Hatton by five points to take his spot in the last four.