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The American's closing 68 gave him a three-shot victory in the PGA Tour's season-ending tournament and with it the first prize of £880,000, the overall FedEx Cup title and an incredible £6.2million bonus.
McIlroy's hopes went up in smoke due to a terrible run sparked by a double bogey at the sixth after he drove into water.
The world No 1 bogeyed 9, 10 and 11 to drop right away before rallying with birdies at 15, 16 and 17.
McIlroy blamed his double-bogey on the sixth on a tired swing, adding on Sky Sports 4: "I was making bad swings at the wrong time and getting punished for them.
"When Billy was making bogey on 10 I thought I had a decent chance and then I three-putt there for the second day in a row and I felt like any chance I had to win the golf tournament went."
Asked about his season overall, McIlroy added: "To win two majors, my first WGC event and give it a real good run in these FedEx events, I'm really proud of myself the way I hung in there and dug deep the last few weeks.
"When I look back on the year as a whole it's been my best year to date so I can't complain."
Jim Furyk was tied for the lead with three to play but faltered at the finish and shared second place with McIlroy.
On a dramatic final day, the key moment came at the 16th hole when Horschel looked set to fall back into a tie with Furyk before sinking a 31 foot putt for par.
When Furyk bogeyed 17 after a poor approach, Horschel had breathing space and a three-putt at the last from the veteran American meant Horschel, who also won last week's BMW Championship, teed off at the last with a three-shot lead.
Horschel closed out victory in style with a lovely tee-shot into the heart of the green and two-putted to land his monster payout with a winning score of 11-under.
Chris Kirk, Justin Rose and Jason Day tied for fourth.
Rose twice got within two shots of the lead on the back nine but bogeyed the 13th and 17th at crucial moments on his way to a closing 69.
Things seemed to be going McIlroy's way when he hit a wild drive on the fourth but had a clear shot to the green and ended up holing from 18 feet for birdie.
Horschel followed McIlroy in from 11 feet to remain tied for the lead before edging ahead on the next, where he holed from 18 feet as McIlroy had to settle for par.
Perhaps the decisive moment arrived on the treacherous par-three sixth, where Horschel hit a superb three iron into the heart of the green and then saw McIlroy, attempting to hit two clubs less, pull his tee shot into the water surrounding the green.
From the drop zone McIlroy pitched to 12 feet and two-putted for a double-bogey five and the four-time major winner found more trouble on the ninth, the 25-year-old's wild drive finishing up against a fence separating the par-five from the practice ground.
After weighing up his slim options, McIlroy told caddie JP Fitzgerald: "I'm just going to blast it, see where it goes", and proceeded to try to hit his second shot over a group of trees just a few yards in front of him.
The ball inevitably made contact but rebounded out towards the fairway, but having laid up with his third shot, McIlroy missed the green with his approach and in the end did well to get up and down for a bogey six.
Horschel looked to have given McIlroy a glimmer of hope when he found thick rough off the tee to bogey the 10th, only for McIlroy to then three-putt from 20 feet and also bogey the 11th to effectively end his chances.
Despite winning the final two FedEx Cup play-off events, Horschel will not be heading to the Ryder Cup at Gleneagles in two weeks' time having only struck his golden patch of form after skipper Tom Watson had already announced his wildcard picks.
