The world number one posted his best score of the week, but a 68 for six-under-par 210 was not enough to keep pace with the leaders amid low scoring at Whistling Straits.
McIlroy mixed the stellar with some "patchy" golf in a round highlighted by a 65-foot eagle putt from the fringe at the par-five fifth.
"It was a day that started well and ended well, birdieing two of the last three holes," said the Northern Irishman, who is competing for the first time since he ruptured an ankle ligament while playing football with friends on July 4.
"Got off to a dream start, really. To be four-under through five ... that was a bonus."The stuff in between was a little patchy at times. I hit a lot of good shots, I putted better. There were just a couple of loose ones here and there."
Last year's champion felt he should have gone lower in the ideal conditions."I came off the course definitely thinking there was a really low one there," said the 26-year-old, a four-times major winner. "It's still my best score of the week, but it could have been a lot better.
"I guess it probably shows just a lack of competitiveness, considering this is the first week back in a few weeks."
Overall, though, McIlroy drew a lot of satisfaction from his third-round form.
"If I keep showing improvement each and every day like I have done, it's a good sign going into the rest of the season."
(Editing by Andrew Both)
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