McIlroy had finished third, sixth and 20th in his first three events of 2016 before a missed cut in the Honda Classic last week prompted him to switch to a “crosshanded” putting method he last used in 2008.
The 26-year-old needed 33 putts in his opening 71 but just 25 on Friday and carried on where he left off on Saturday, taking 28 putts in a bogey-free 68 which was the joint second lowest score of the day.
That meant McIlroy turned a two-shot deficit to a three-shot lead over defending champion Dustin Johnston and halfway leader Adam Scott, who carded rounds of 71 and 73 respectively.
McIlroy got up and down from a greenside bunker to birdie the par-five first and picked up another shot from seven feet on the fifth, before a birdie on the eighth - despite finding two bunkers - took him into the outright lead for the first time.
Scott had bogeyed the difficult fourth and missed from nine feet for eagle on the eighth, although the tap-in birdie meant he trailed playing partner McIlroy by a single shot as he looked to claim back-to-back wins following his victory in the Honda Classic.
McIlroy extended his lead with a birdie on the 10th and when Scott bogeyed the 13th after failing to get up and down from a greenside bunker, the Northern Irishman was three shots clear.
Scott responded with one of the shots of the week on the 14th, his recovery from a fairway bunker catching the edge of the trap but still finishing just nine feet from the hole.
The former Masters champion duly converted for birdie and was joined on 10 under by Johnson, who had picked up a shot on the short par-four 16th.
However, Johnson then bogeyed the last after a wayward drive and miss from close range and Scott did likewise on the 17th, meaning McIlroy’s par save from a greenside bunker on the last put him firmly in pole position in pursuit of a third WGC title.
Phil Mickelson, Danny Willett and Bubba Watson were five shots off the pace on seven under, with Sergio Garcia, who was second to Scott at the Honda Classic, fellow Spaniard Rafael Cabrera-Bello and India’s Anirban Lahiri two shots further back.
McIlroy, who was met by a rules official before signing his card to make sure he had not broken any rules in tightening his driver on the 18th, said: “I’m pretty sure that’s my first bogey-free round of the year. To do it in a round like this is very pleasing.
“I’ve been saying all week that I’ve been making the birdies and I’ve been hitting the good shots. I’ve just been making too many mistakes. So to play the last 36 holes on a golf course like this with just one bogey on the card is really what I wanted to achieve this week. I feel really good about my game.
“My ball-striking, my driving, that really hasn’t been an issue this year. That’s been where I wanted it to be. But my scrambling and my putting have needed work.
“I feel like the practice that I’ve put in over the last few weeks is really starting to pay off. Just look at some of the saves I had out there today and some of the big par putts - those were the things that were missing over the past three or four tournaments.
“And to be able to correct that and go out and play in a final group on a Saturday in a golf tournament like this on a golf course like this, and play bogey-free, it gives me a lot of confidence going forward.
“There’s not many positives from a missed cut (at the Honda Classic) but I made nine birdies over the first two days on a tough golf course in tough conditions. I knew the good stuff was in there. It was just about trying to eradicate the bad stuff, the loose shots, the mental errors, the mistakes.
“I didn’t feel like there was much of a disappointment after last week. To be honest, to miss a cut and be able to sleep in your own bed, it’s not too bad. Gave me a couple extra days to practice, and maybe if I didn’t have those couple of extra days, I wouldn’t have found something in my game that I really liked to go forward with. There’s always a silver lining.”
World No 1 Jordan Spieth is 10 shots off the lead after a 73, but at least had the distinction of posing an interesting rules question.
The Masters and US Open champion asked a rules official early in his round if he was allowed to dampen the bottom of his putter to prevent it slipping on the slick greens.
“I’ve spoken to commentators, players and nobody knew the answer if you can do it,” Spieth said. “I didn’t know if it was legal so I’ve never done it on the golf course (during a tournament round), so I asked an official.
“It was a split on the decision so they called the USGA and he said that the USGA was going to talk about it further, but for now we’re going to rule that you cannot do it.”
Spieth was told he could use a towel to clean his club and if the towel was wet that would not be a violation, but was advised not to lick his thumb and apply it to the bottom of his putter.
Russell Knox is sitting joint-17th after the Scot followed a pair of 71s with a third-round 72.