A stroke in front overnight heading into what is traditionally known as 'moving day', the British Open champion birdied three of the last four holes on a receptive, rain-sodden Valhalla Golf Club layout to card a four-under-par 67.
In pursuit of a third consecutive victory on the PGA Tour, McIlroy fended off a series of challenges to keep his position at the top of a tightly congested leaderboard as he posted a 13-under total of 200 in the year's fourth and final major.
Austrian Bernd Wiesberger, one of six players who held at least a share of the lead in a wildly fluctuating third round, was alone in second place after matching the day's best score with a 65.
"It's not the biggest lead I've ever had, but I'm still in control of this golf tournament," said world number one McIlroy, who had been two strokes clear after seven holes before bogeying the par-three eighth.
"It's a great position to be in going into tomorrow."
McIlroy was delighted with his finish to the round, sinking a 20-footer on 15, a two-footer on 16 and getting up and down from a greenside bunker to birdie the par-five last.
"I just knew that I needed to make a couple coming down the back nine to keep the lead I had or at least be tied for the lead going into tomorrow," said the 25-year-old Northern Irishman.
"The two birdies on 15 and 16 were huge. To get up and down out of the bunker on 18 was big.
"It's not like it's that huge of a difference between tied for the lead and being one ahead going into tomorrow, just sort of makes you feel better about yourself going to bed tonight."
Surprise package Wiesberger, who had missed the cut in four of his previous five major appearances, was still coming to terms with his lofty position going into the final round.
"I didn't expect any of this really coming into this week," said the 28-year-old from Vienna, a two-time winner on the European Tour. "I knew I was prepared well and the course really suits my eye.
"So far I've taken advantage of this and it's great to finish the round with three birdies in a row, basically tap-in birdies as well.
"That gives me hopefully good momentum going into tomorrow. It's a new situation for me in a major championship."
American 'young gun' Rickie Fowler, a top-five finisher at each of the year's previous three majors, was at 11 under after firing a 67 with 2005 PGA Championship winner Phil Mickelson (67) and Australian Jason Day (69) a further stroke adrift.
Left-hander Mickelson, who played with Wiesberger in the third round, vaulted into contention for a sixth career victory in the majors with four birdies in the last five holes.
"It's so fun for me to be back in the thick of it, have a chance, being in contention heading into Sunday," said the American. "My game feels so close to clicking. And when I say clicking, shooting really low."
Former British Open champion Louis Oosthuizen of South Africa (67) and Swedish world number four Henrik Stenson (67) were among a group of four at nine under on a high-quality leaderboard that sets up an intriguing battle for the title.
However, most eyes in Sunday's final round will be focused on McIlroy, who has produced spectacular form over the past month and came into this week as an overwhelming favourite.
The Northern Irishman completed a wire-to-wire victory at last month's British Open before winning the WGC-Bridgestone Invitational last Sunday in his next start.
"I came from three shots behind last week," said McIlroy. "The guys got pretty close to me at the (British) Open Championship. They got close to me again today, and I was able to respond like I did on the back nine.
"I'm loving it. It's where I want to be. It's the best place to be in the golf tournament."
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