The 22-year-old Northern Irishman's joint best-of-the-day 66 at the Honda Classic in Florida today took him to 11 under par - and his two closest challengers entering the final day were players ranked 269th and 216th.
They were Americans Tom Gillis and Harris English, the former a 43-year-old self-confessed journeyman and the other a 22-year-old rookie professional.
England's Justin Rose had shared the halfway lead with Gillis, but had to scramble for all he was worth for a one-over 71 that left him in joint fourth place and four behind.
McIlroy has to win to dethrone Luke Donald at the top of the rankings, just as he did going into last week's Accenture Match Play Championship in Tucson.
He made it all the way through to the final there, but then lost to American Ryder Cup player Hunter Mahan.
McIlroy looked a class act as he hit back from a sticky patch midway through the front nine.
He had a hat-trick of birdies starting on the long third, two-putting there and then holing from 22 and 10 feet.
He was two clear at that point, but promptly bogeyed the next two, coming up short of the green on the sixth and three-putting the short seventh.
That gave Gillis the lead again and he stayed there with a remarkable run around the turn.
On the eighth he took a shoe and sock off and rolled up his trouser leg to play his ball out of the edge of the water and holed from 33 feet for par.
He followed that with a 28-footer for another par, birdied the 10th from five feet and then rescued a further par from 33 feet again on the next.
McIlroy had birdied the 11th from 45 feet after his approach from the rough only just carried over the lake and a glorious nine-iron to five feet at the 15th led to him regaining top spot on his own when Gillis failed to get up and down from sand there.
Bunkered in two at the par-five last, McIlroy splashed out 12 feet past the flag, but made it to complete another fine day's work.
McIlroy said: "This is where I want to be. This is why I play golf, to put myself in contention to win tournaments and try to become the best player in the world."
Asked if he had learnt anything from last week he stated: "It's a different format and the approach is slightly different.
"I didn't have as much time to think about it there because I went straight from the semi-final (a win over Lee Westwood) into the final.
"I've just got to try to approach it like any other tournament."
Compatriot Graeme McDowell's 69 put him in a share of 10th place, but he was seven back, while England's little-known Nationwide Tour graduate Gary Christian was one further behind following a second successive 67.
Tiger Woods was in 18th place on two under after a 69 and Westwood (70) one under after playing with the former world number one for the third day in a row.
Woods threatened to climb into the hunt when he birdied the third, fourth and seventh, but he never had another all day and bogeyed the 13th.
"I putted great and I was close to putting a low one up there," he said. "I felt like I could post five under par for the day or something like that and get myself within reach."
On McIlroy possibly being 18 holes from the world number one spot he added: "I played with him in Abu Dhabi the first two days [last month]. He's still learning.
"He's developed a lot, but also he's got a lot to learn too, which anyone that age does."
With the possibility of thunderstorms in the Palm Beach Gardens area on Sunday afternoon tournament organisers decided to move tee times forward.
McIlroy was due to tee off at 10.30am local time in a threeball with Gillis and English. Winds as high as 25 mph were also expected.