"It was hard to get any rhythm because Phil was here, there and everywhere, so I was waiting a lot," Northern Irishman McIlroy told reporters after a steady one-under-par 70.
"It probably shouldn’t have affected me but it did a little bit."
McIlroy and Mickelson will start the final round two strokes behind American leader Justin Thomas, and one adrift of world number one Dustin Johnson.
If world number three McIlroy wins, he will go back to the top of the rankings as long as Johnson finishes worse than solo fourth.
Mickelson, meanwhile, has his sights set on ending a victory drought that stretches back to the 2013 British Open at Muirfield.
The 46-year-old was fortunate to be so close to the lead, after a stretch of poor driving and a couple of favorable rulings.
At the 10th hole his ball was ruled to have been picked up by a spectator, which afforded him a free drop instead of a stroke-and-distance penalty.
At the next hole his drive ended under a bush, almost unplayable, but he was allowed a free drop after convincing rules official Slugger White that he would have been forced to stand on a sprinkler to take the shot he wanted.
"I know it looks bad. I’m just telling you that’s the truth," Mickelson told White, who said he would have to take the golfer at his word.
Mickelson escaped with an unlikely par and was lucky to drop only one shot at the 12th hole after finding another bush with his tee shot.
"I had a complete meltdown and lost all focus in my game for a nine-hole stretch," Mickelson said after shooting 68.
"I fought hard and showed a lot of heart trying to just stay in it."
(Reporting by Andrew Both in Cary, North Carolina, editing by Gene Cherry)
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