American Ryan Moore was in second place on 10-under 132 after shooting a 68 at the FedExCup series event.
"I'm very pleased with how I played today, how I played yesterday as well, and I'm in a great position," McIlroy told reporters. "I got off to a nice start and just kept the momentum going.
"Everything seemed to work pretty well out there. I felt like I drove the ball a bit better today and hit more fairways, which gave me some more opportunities to make birdies, and I was putting well enough to take a few of those."
Overnight leader Noh Seung-yul of South Korea, who opened up with a 62, could only manage a 71 on Saturday as he shared third spot with Americans Jason Dufner (66) and Chris Kirk (70).
Former world number one Tiger Woods is among the afternoon starters. He carded a 64 on Friday.
McIlroy started on the back nine and claimed his first birdie with a nine-foot putt on the 12th.
The Northern Irishman almost holed out from 161 yards for an eagle on the 14th, tapping in for the second of six birdies in the round.
Another perfect approach on the 15th to inside five feet yielded dividends before the U.S. PGA champion coaxed in an 11-foot eagle putt on the 18th to turn in 30 strokes.
McIlroy then birdied the first from 18 feet before dunking his approach on the second into water and taking a bogey.
He dropped another shot at the third before rallying with birdies at the fourth and fifth.
The leading 70 players on the FedExCup points list after this event advance to the BMW Championship, with the top 30 then progressing to the Tour Championship finale in Atlanta where the overall points winner pockets a $10 million bonus.
