McIlroy had two eagles and four birdies in a six-under-par 66 and with a 12-under total of 204, was poised to strike Sunday for a long coveted green jacket that would see him become just the sixth man to complete a career Grand Slam.
McIlroy's first eagle of the day was at the par-five second, part of six straight threes to open his round - a first in Masters history.
His second eagle at the par-five 15th, where he stuck his approach six feet from the pin, was the first of the day there and pushed his lead back to four strokes after it had dwindled to one thanks to bogeys at the eighth and 10th.
He'll play in the final group on Sunday with US Open champion Bryson DeChambeau, who birdied three of the last four holes for a three-under 69 and a 10-under total of 206.
Canadian Corey Conners was alone in third after a two-under-par 70 for 208- two strokes clear of former Masters champion Patrick Reed and last year's runner-up Ludvig Aberg.
Two off the pace to start the day, McIlroy catapulted himself past overnight leader Justin Rose and Bryson DeChambeau - who tied Rose at eight-under with a birdie at the first.
But the final pair of Rose and DeChambeau were finishing up on the first green when McIlroy gained the lead, holing out from 18 yards at the par-five second.
McIlroy, tied with Corey Conners to start the day, had taken advantage of a monster drive at the first, where he rolled in a 10-foot putt to secure a birdie.
McIlroy kept the magic flowing with a seven-foot birdie putt at the third. After a two-putt par at the par-three fourth, he drilled an 18-foot birdie putt at the par-four fifth.
He two-putted for par at the par-three sixth to put a sixth straight three on his card.
That run ended at the par-four seventh, where he was deep in the trees off the tee and muscled a mighty second shot 152 yards to the left of the green, from where he got up and down for par.
McIlroy became the first player in Masters history with threes on the first six holes.
McIlroy just missed the Masters record of seven consecutive threes in a round - set by Jodie Mudd in 1987 - but he led by as many as four before his first bogey of the day at the par-five eighth - where his tee shot landed in the face of a fairway bunker.
It was McIlroy's first dropped shot since a double bogey on 17 on Thursday. He missed a golden chance to regain the stroke when his five-foot birdie attempt at the ninth slid by on the left.
But McIlroy, who can become just the sixth man to complete a career Grand Slam with a Masters win on Sunday, was two ahead of DeChambeau as he headed into the back nine.
McIlroy said before the round he would try to keep his eyes off the leaderboard and focus on the task at hand.
Don't force the issue
"It's the same mindset today, go out there, take care of what I'm doing, don't look around," he said. "Just letting the score come to me, not trying to force the issue too much."
Reigning US Open champion DeChambeau rolled in a 35-foot birdie putt at the first, and two-putted for eagle at the second.
Afer bogeys at the third and seventh - where he couldn't get a 14-foot par putt to drop - DeChambeau birdied the eighth, tapping in after missing his long eagle attempt.
Rose, seeking a second major title 13 years after his US Open triumph, struggled to get anything going. He missed a nine-foot birdie chance at the second and three-putted for bogey at the fourth. After a bogey at the seventh he finally nabbed his first birdie of the day at the eighth.
That moved him to seven-under, tied with Conners, who was one-over for the day through six holes but closed the front nine with back-to-back birdies.
“Defending champion Scottie Scheffler started the day three shots off the lead and tied with former British Open champion Shane Lowry, Tyrrell Hatton and Matt McCarty.
Scheffler birdied the second, but the world number one was scrambling at almost every hole and dropped a shot at the seventh -- where he was in the rough off the tee and in a greenside bunker from there.
He was five-under through 10 and needing to make something happen to put himself in position to join Jack Nicklaus, Nick Faldo and Tiger Woods as the only players to win back-to-back Masters titles.