Englishman Hatton, 28, showed nerves of steel in difficult conditions over the last seven holes for a two-over-par 74 in the final round to hold off the challenge of Australia’s Marc Leishman.
Hatton was playing in only his second event since undergoing wrist surgery at the end of last year.
South Korea’s Sungjae Im finished a further shot back in third place, while world number one Rory McIlroy, who started the day joint second, tied for fifth after a 76.
Bryson DeChambeau carded a one-under final round to claim fourth place, while fellow Americans Keith Mitchell and Joel Dahmen also shot 71s to finish alongside McIlroy and New Zealand’s Danny Lee.
Hatton won his fourth European Tour title in a six-man play-off in the Turkish Airlines Open in November and shortly after playing in the season-ending event in Dubai a fortnight later had an operation on his wrist.
"Oh my God. I can't believe it." 🏆March 8, 2020
He held a two-shot lead going into the final round at Bay Hill and overcame a disappointing start after bogeying at the first and fifth holes with birdies at the seventh and eighth.
Hatton then double-bogeyed the 11th, but with the pressure on he made par on each of the last seven holes to claim victory.
England’s Matthew Fitzpatrick produced the round of the day, shooting a three-under 69, which included five birdies and a double-bogey at the 17th, to climb 27 places and finish tied for ninth.