McIlroy carded a closing 68 at Valhalla to finish 16 under par, one shot ahead of Phil Mickelson after a remarkable final day which finished in near-darkness, with the lights blazing from the clubhouse behind the 18th green.
Rickie Fowler and Henrik Stenson had been part of a three-way tie for the lead with Mickelson on the back nine but dropped shots on the closing stretch to finish two behind McIlroy on 14 under.
A torrential downpour which flooded the course and caused a delay of almost two hours meant it was a race against time to get play finished, so much so that Mickelson and Fowler stood aside on the 18th to allow the final group to tee off.
McIlroy's drive finished dangerously close to the water to the right of the fairway, but a closing par was enough for the 25-year-old to become the first player since Padraig Harrington in 2008 to win back-to-back majors, his victories in the Open Championship and US PGA also sandwiched by a first World Golf Championship win in the Bridgestone Invitational last week.
Lifting the Wanamaker Trophy for the second time also makes the Northern Irishman the third youngest player after Tiger Woods and Jack Nicklaus to win four majors, just one less than the total won by the late Seve Ballesteros and two behind Nick Faldo.
It was the fourth time McIlroy had held the 54-hole lead in a major, the first leading to heartache in the 2011 Masters when he was four ahead entering the final round at Augusta only to collapse to a closing 80.
Two months later he bounced back in spectacular style to win the US Open by eight shots at Congressional before winning the 2012 US PGA by the same margin at Kiawah Island.
Last month he led from start to finish at Royal Liverpool, taking a six-shot lead into the final round before going on to win by two from Sergio Garcia and Rickie Fowler.
This time he started the day with a one-shot lead but dropped two shots in his first six holes and trailed Fowler by three as he reached the turn, Fowler having recovered from a bogey on the second with four birdies in his next five holes.
The par-five 10th had cost McIlroy a double-bogey seven on Thursday but three days later he hit a fairway wood to seven feet and holed the eagle putt to get back into contention in stunning fashion.
Mickelson then birdied the 11th to join his playing partner Fowler in the lead, the pair exchanging fist-bumps as they walked to the 12th tee, and Stenson made it a three-way tie with a birdie on the 13th.
Stenson had offered a prayer of thanks to the golfing Gods when his approach had just carried the water, only to three-putt the next to drop out of the lead and effectively end his chances of a first major title.
McIlroy missed good birdie chances on the 11th and 12th, the latter after seeing Mickelson in the group ahead hole from 30 feet across the green for an unlikely par.
But the world number one made no mistake from eight feet on the 13th to get back into a share of the lead with five holes remaining.
Fowler was the first to crack under the pressure after a wayward tee shot led to a bogey on the 14th, and when Mickelson bogeyed the 16th, McIlroy was back in the outright lead for the first time since the third hole.
As the light quickly faded, McIlroy delivered the killer blow with a birdie from nine feet on the 17th to enjoy a two-shot lead playing the last.
Mickelson did not seem happy with being asked to make way for McIlroy on the 18th but almost holed his pitch shot for an eagle, the birdie forcing McIlroy to make par for the win.
1989: Born on May 4 in Holywood, Northern Ireland.
2005: Plays in his first professional European Tour event as a 16-year-old at The Forest of Arden. In July, shoots a course-record 61 on the Dunluce links at Royal Portrush.
2007: July - Shoots opening round of 68 in the Open at Carnoustie, the only bogey-free round of the day. Goes on to tie for 42nd and wins Silver Medal as leading amateur.
September 18 - Turns professional.
October - Finishes third in his second pro event, the Alfred Dunhill Links Championship. The following week, he secures his card for the 2008 season by finishing joint fourth at the Open de Madrid.
2008: September 7 - Takes a four-shot lead into the final round at the Omega European Masters in Switzerland but bogeys the 18th to tie with Jean-Francois Lucquin, who goes on to win in a play-off. Finishes the season in the top 100 of the world rankings and ranked 36th on the European Tour Order of Merit.
November - Finishes second in the UBS Hong Kong Open, helping him become the youngest player ever to make the top 50 in the world rankings.
2009: February 1 - Wins first professional title at the Dubai Desert Classic by one shot from Justin Rose.
November - After finishing second to Lee Westwood in the Race to Dubai, enters the world's top 10 for the first time.
2010: May 2 - Secures first PGA Tour win with victory in the Quail Hollow Championship. His final-round 62 is a new course record. Becomes the first
player since Tiger Woods to triumph on the PGA Tour prior to his 21st birthday.
July 15 - Shoots 63 on the opening day at St Andrews to lead the Open. Rounds of 80, 68 and 69 see him finish joint third.
October 4 - Wins a crucial half point against Stewart Cink to help Europe win the Ryder Cup at Celtic Manor.
2011: April 10 - Takes four-shot lead into final round of the Masters at Augusta but shoots a closing 80 to finish tied 15th.
June 19 - Wins US Open at Congressional by eight shots for his first major title.
2012: March 4 - Wins the Honda Classic in Florida to claim the world number one ranking, although he later loses it to Luke Donald.
June - Misses the cut in the defence of his US Open title. Finishes a lowly 60th in the Open Championship at Royal Lytham the following month.
August 12 - Lands the US PGA title at Kiawah Island, winning by eight shots.
September 30 - Having almost missed his singles match due to a timekeeping issue, McIlroy beats Keegan Bradley as Europe recover from 10-6 behind on the final day to win the Ryder Cup at Medinah.
October/November - Second place at the BMW Masters in Shanghai is followed by third place at the Barclays Singapore Open as McIlroy wins the Race to Dubai with two events remaining.
November 25 - Wins the DP World Tour Championship in Dubai, beating Justin Rose by two shots after five closing birdies.
2013: January 14 - Signs a multi-year sponsorship deal with Nike, reportedly worth up to £156million.
March - Walks off course in second round of Honda Classic, telling reporters he was "not in a good place mentally." His management company later issued a statement saying he was suffering from toothache.
June - Bends his nine-iron out of shape in frustration in the final round of the US Open at Merion, finishing 41st.
July - Labels his own play as "brain dead" after missing the cut in the Open at Muirfield.
September - Sets up his own management company, Rory McIlroy Inc, prompting a legal battle with former company Horizon Sports.
December - Wins first tournament of year in Australian Open.
2014: May - Wins BMW PGA Championship at Wentworth after starting the final round seven shots behind. Five days earlier he had called off wedding to Caroline Wozniacki after invitations had been sent out.
July 20 - Wins third major title by two shots from Sergio Garcia and Rickie Fowler in the Open Championship, leading from start to finish at Royal Liverpool.
August 3 - Comes from three behind Garcia in the final round to win first World Golf Championship title in the Bridgestone Invitational.
August 10 - Wins third tournament in succession and second major in four weeks in the US PGA Championship at Valhalla.
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