On a windy closing day at Bay Hill in Orlando, the 24-year-old from Oban covered his last 10 holes in four-under for a level-par 72.
He was one of just seven players to card par or better in the final round and finished in a tie for 36th behind Bryson DeChambeau with a two-over 290 total in the $9.3 million event.
MacIntyre had started the final round sitting 61st following a third-round 76, the tone for which was set when he hit his opening tee shot out of bounds and started with a triple-bogey 7.
The left-hander took his revenge on that hole as he opened with a birdie from six feet in the final circuit only to have the wind taken out his sails straight away following a double-bogey 5 at the next.
A visit to the water off the tee led to another double-bogey at the par-5 sixth before he found himself four-over for the day after dropping a shot at the seventh.
That left MacIntyre facing a big test of character, but, not for the first time in his career, he responded positively with his back against the wall.
The Scot holed a 21-footer for a birdie-3 at the ninth before hitting his approach from 129 yards to three feet at the next for another gain.
His third birdie in four holes came from an up and down from a greenside bunker at the long 12th before he followed a two-putt gain from 66 feet at the 16th by saving par from 24 feet at the last.
"Bit of everyhing this week,” wrote MacIntyre on Twitter of his effort, which is set to see him climb one spot to 42nd in the updated world rankings.
The strong finish saw MacIntyre end the event one ahead of Martin Laird and seven in front of Russell Knox.
Laird, the 2011 winner, had been second on eight-under at the halfway stage but tumbled down the leaderboard after closing rounds of 76-79.
Knox also signed off with a 79 that included an eagle but also two double-bogeys.
The trio are also in the field for this week’s The Players Championship at TPC Sawgrass in Ponte Vedra Beach.