McIlroy charged out of the blocks with two birdies in his first four holes but as gusty winds began to whip across the course, and McIlroy’s putter cooled, scoring became difficult.
Having dropped just one shot in his opening 54 holes, McIlroy’s second bogey of the week came at the sixth hole just as another Englishman, Ross Fisher, began to surge.
Fisher eagled the second to grab the outright lead in the group behind McIlroy while in the group ahead Fleetwood looked to be treading water with two birdies and a bogey over the outward nine.
But the reigning Race to Dubai champion was far from done and, starting with a birdie at the 10th, he reeled off six back nine birdies to get to 22-under with a scintillating 7-under 65.
The relentless pressure from Fleetwood took its toll on Fisher who, after going to the turn 4-under and looking in an almost unassailable position, dropped his first shot of the day at the 10th.
A run of four pars followed with the fatal error coming at the 15th with a second bogey of the day.
A birdie at the next was too little too late and after making back-to-back bombs on 15 and 16 Fleetwood sealed the deal with a seven-foot birdie putt on the 18th.
The 27-year-old seemed almost as shocked by his fourth European Tour title as those he’d left in his wake, telling TV commentator Andrew Coltart his first title defence had been an emotional affair.
“I feel a lot more emotional, actually, than last year,” he said. “I don't know why. I just really wanted to win this one. It's important that - I had the year of my life last year.
“I know everybody has been talking about it, and just backing it up is the next big thing, really.
“It's a weird feeling coming to defend a trophy because it's yours and you don't want to give it away. So keeping a hold of it for another year is very nice.”
For his part, Fisher was disappointed but paid full credit to Fleetwood for a stunning round in tough conditions.
“I felt like I was hitting good shots but it was just very tricky to get close to the pins,” he said.
“The wind was strong. It was gusty, it was left-to-right, it was helping, it was into. It was tricky, and then obviously 15 was disappointing.
“Thought I hit a better shot than that. Just unfortunately just didn't push it enough.
“So hats off to Tommy. I don't feel like I've lost a tournament. Tommy's gone out there and shot 65 and he's won it, so all credit to Tommy.”
Scott Hend was the leading Australian after a third successive 69 lifted him to 10-under and a share of 22nd.
Sam Brazel and New Zealand’s Ryan Fox both went backwards Sunday to finish the week 7-under and T32, Jason Scrivener was also over par in the final round to be 5-under and T48.
Jason Norris, Wade Ormsby and Andrew Dodt all missed the 36-hole cut.
SIGNATURE HOLES - 9TH AT MT XAVIER GOLF CLUB:
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