He completed a third-round 68 with a magnificent birdie at the 18th, playing an awkward bunker shot and then sinking a 25-foot birdie putt.
The famous bunker shot was fully 60 feet from the pin and was lofted 12 feet into the air before it rolled into the cup.
After Havret had pitched to 20-feet from the flag, McIlroy conjured up his final piece of magic by holing his bunker shot to round out victory on 12-under 268.
The Scot rounded off a memorable day by holing a 40-yard bunker shot for eagle at the final hole to finish on 21-under par and move a step closer to a first European Tour win since 2004.
His tee shot on the 17th left him out of position and after finding a greenside bunker he dropped his first shot of the day.
Els finds the bunker with his second shot but another magnificent recovery earns the South African a par four and a share of the points with Garcia.
Furyk, the 2003 winner, buried his second shot in a bunker dashing his chances.
George's last year, won on the second hole with a birdie after a remarkable approach shot from the bunker.
Feng closed within a shot with a short birdie putt at No. 16 but she hit her tee shot in the bunker at the next hole and bogeyed.
He birdied the sixth then picked up a superb eagle on the par-four seventh, holing with a seven iron after having again driven his tee shot into a bunker.
William McGirt was playing his shot from the fairway bunker on the other side and had no idea what Garcia was doing.
He went for the green and his 3-iron struck a tree and dropped straight down, his next shot plugged in a bunker and he make double bogey to lose by one.
Playing the 18th holes once again, Harrington was the only one of the three hopefuls to find the green in regulation in the play-off with Hamill putting his approach shot into a greenside bunker.
Webster moved alongside Manassero with a seven-under 64 which included a spectacular eagle at the par-five 13th, which saw his second shot from a fairway bunker strike the flag, leaving him with a six-foot putt for his three.
His chip shot then hit the edge of a greenside bunker, rolling into the sand, and he failed to get out of there on his next shot before finally blasting to 6 feet.
But he took three shots from inside a radius of about 5 yards after his approach shot from a left fairway bunker stopped behind the hole.
The 53-year-old carded five birdies on his back nine, including one from out of a bunker at 17, to claim a two-shot lead.
Woods pulled off his shot, and then blasted out of the bunker to about 10 feet and made birdie to take the lead.
Garcia finds the sand with his tee-shot, then an untidy second lands in another bunker in front of the green.
Instead of laying up, he drilled a 5-wood into the bunker left of the green, setting up a simple sand shot and a birdie he didn't even need.
Havret found sand off his tee shot and was forced to lay up short of the green with his second shot, but McIlroy also ended in a greenside bunker with his approach.
He was seized off a crowded school bus Jan. 29 after authorities say the gunman shot the driver dead and took him to the bunker where he was held until Monday's rescue.
Harrington made a shaky start to the second practice session on Wednesday, firing his opening tee shot into the gallery while his second effort found a bunker.
He followed that with a mid-iron from a fairway bunker on the 16th to four feet for yet another birdie and, at that stage, a four-shot lead over Masters champion Mickelson.
BBC: Rory McIlroy breaks record to win maiden PGA Tour title
And it was Germany's Kaymer who ended the third round with the best chance of victory after holing five birdies before dropping his only shot of the day at the ninth - his final hole - where he drove into the fairway bunker.
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