INDIANAPOLIS, Indiana, Sept 9, 2012 (AFP) - McIlroy, who won the Deutsche Bank Championship last week by one stroke, finished with a 20-under par total of 268, two shots in front of Phil Mickelson and Lee Westwood.
McIlroy, the world number one who claimed the second major title of his career at the PGA Championship last month, nabbed his fourth US tour title of the season and the sixth of his career.
England's Westwood carded a 3-under 69 at Crooked Stick, while Mickelson posted a 70 for 270.
McIlroy had six birdies on the day, breaking out of a four-way tie for the lead with birdies at nine and 10. Two more birdies at 15 and 16 gave him enough of a cushion to make his bogey at 18 irrelevant.
McIlroy became the first player since Tiger Woods in 2009 to win in successive weeks on the US tour and he joined Woods and Jack Nicklaus as the only players to win at least six PGA Tour events before his 24th birthday.
Woods, never a serious threat to the lead, finished three off the pace after a 68 for 271. He was tied for fourth with Robert Garrigus (69).
The top 30 players in the playoff standings now advance to the finale, the Tour Championships at Eastlake in Atlanta.
Defending FedEx Cup playoff champion Bill Haas was among those who didn't make it after a round that included a double-bogey and seven bogeys.
Leading final-round scores here on Sunday from the $8 million BMW Championship (USA unless noted, par-72):
268 - Rory McIlroy (NIR) 64-68-69-67
270 - Phil Mickelson 69-67-64-70, Lee Westwood (ENG) 68-65-68-69
271 - Robert Garrigus 67-69-66-69, Tiger Woods 65-67-71-68
272 - Dustin Johnson 68-67-67-70, Adam Scott (AUS) 68-68-66-70
273 - Vijay Singh (FIJ) 65-66-69-73
274 - Jim Furyk 69-70-67-68
275 - Ryan Moore 66-66-73-70, Bo Van Pelt 64-69-71-71
276 - Zach Johnson 67-69-68-72, Chris Kirk 68-68-69-71, Ian Poulter (ENG) 68-68-69-71, Bubba Watson 69-71-71-65
278 - Greg Chalmers (AUS) 74-70-68-66, Tom Gillis 69-67-73-69, Padraig Harrington (IRL) 70-65-70-73, John Huh 70-66-73-69, Troy Matteson 70-66-71-71, Seung-Yul Noh (KOR) 68-66-73-71, Louis Oosthuizen (RSA) 68-69-68-73, Justin Rose (ENG) 67-70-70-71
279 - Ben Curtis 70-69-68-72, Sergio Garcia (ESP) 69-69-71-70
280 - Kevin Na 72-71-68-69, Steve Stricker 68-73-68-71
281 - Luke Donald (ENG) 66-72-72-71, Jason Dufner 72-67-73-69, Ernie Els (RSA) 68-71-69-73, Geoff Ogilvy (AUS) 68-71-74-68, Charl Schwartzel (RSA) 69-68-72-72, Brendon de Jonge (ZIM) 71-66-71-73