Molinari had four birdies on the front nine and four more after the turn, including a 44-foot birdie putt on the 18th hole that sealed his third PGA Tour victory.
"Incredible", Molinari said. "It's high up there with the best wins I've had".
This time, he was in good position just one shot behind Fitzpatrick.
Molinari really had nothing to worry about.
Harding got down in two from the front of the green on the par five 18th and then had to wait and see if anybody could catch him.
Molinari canned a 44ft birdie putt on the last hole at Bay Hill to card a closing 64 and post 12 under, which ultimately gave him a two-shot victory over Fitzpatrick.
Molinari was four strokes ahead of a large group in third place that included defending champion Rory McIlroy, who had also completed 11 holes.
"But at the moment in time you don't want to drop shots". Rarely did either hit approach shots close enough to offer legitimate scoring chances. I get into the events that I'd like to be into again, the schedules change, I'm no longer having to pick and choose.
Molinari drained more than 146 feet of putts - 32 more than Fitzpatrick and McIlroy combined.
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"I thought there was an outside chance and just started making putts", Molinari told NBC television about his mindset after he had teed off five strokes from the lead. "Yeah, I was confident already that my game was at a nice point but obviously it's nice to show it like this on a Sunday". Known for his superb ball striking and solid play, Molinari made a nice living and hoisted the occasional trophy.
Asked what had elevated his game over the past year, he said confidence had a lot to do with it.
Im took one of three available spots for the British Open to those not yet qualified with the others going to South Korean Kang Sung and American Keith Mitchell, who shared sixth on 280 with Northern Ireland's McIlroy and England's Matt Wallace. "I took a longer break after previous year". He played in the final round of the BMW PGA Championship at Wentworth tied with McIlroy, closed with a 68 and won by two. He became the first European to win all five matches at the Ryder Cup.
Birdies on the 10th and 12th put him back in contention and further birdies at the 15th, 17th and 18th handed him a two shot lead at 13 under after a 66.
"And (now) I know I can register low scores on every golf course". For Frankie Molinari, it has proved the place where the dream goes on. He had gone out on a tough day and performed at a level no one came close to matching. He had two birdies, two bogeys and a 72 to tie for sixth. The top 64 players after The Players Championship will qualify for Austin, with Nos. The next time, he hopes the experience is not quite so long and painful.
Francesco Molinari wasn't supposed to be a factor at Bay Hill on Sunday. Neither act was a big deal for the reigning Open champion.
"I got everything out of it", he said.
The victory is a fifth in nine months and four different countries worldwide for 33-year-old Harding, who recorded successive Sunshine Tour wins in May and repeated the feat on the Asian Tour in July.
"I said this after I won the Open Championship previous year, I didn't enjoy it - that half an hour - at all and I didn't enjoy today at all watching the other guys", he said.