Sergio Garcia again did not drop a shot in a second successive 67 and shares second, while Tiger Woods moved up to seven under after a 66 with no bogeys.
World number one Lee Westwood, playing in the same group as Woods, dropped two shots in a 70 and is five under.
Martin Kaymer, the world number two, is one further back after a round of 71.
McIlroy edged clear of the field after laying up short of the water at the dangerous closing par five and playing a wedge from 103 yards to seven feet to set up his third birdie on the back nine.
Resuming on one under par following his closing eagle on the opening day, Woods began his second round from the 10th hole and birdied the 12th, 13th and 18th to reach the turn in a three-under 34.
The 35-year-old American added yet another birdie on the second despite driving into the rough and continued his charge with a 25-footer on the short fourth.
And a wondrous approach to two feet at the 485-yard par-four sixth brought the current world number three his sixth birdie of the day.
Tiger Woods
Woods looked to be regaining his best form with some more accurate play
It was a fine resurgence from Woods, who after five holes of his first round was two over and tied for 96th.
"I played myself right back into the tournament. I felt I hit the ball a lot better and the greens were absolutely perfect," he said.
"It was steady. I didn't make as many mistakes as yesterday and I felt it was important to post a number."
Westwood, who missed the cut in Abu Dhabi last week, collected four birdies, picking up a shot at the 18th where he made six on Thursday, but was frustrated with his position in a large group sharing 11th place.
"I'm a bit disappointed with the way I've hit it the first two days," he commented. "You have chances out there - you've just got to be on your game."
South African Thomas Aiken, who also started on the 10th, birdied his first hole of the round and was to add a further five with his only blemish a bogey on the par four 16th.
Defending champion Miguel Angel Jimenez missed a short birdie chance on the final green but comfortably progressed through to the final two days after a round of 70 took him to two under.
Ryder Cup captain Jose Maria Olazabal was also two under the card after three birdies in six holes in a round of 69, but playing partner Colin Montgomerie took a double bogey at the ninth, his closing hole, and finished at five over, well outside the cut line.