World number two McIlroy, who began his round at the par-four 10th hole at Aronimink Golf Club and was dealing with a blister on his right pinky toe, hit a tree with his tee shot, barely got his second shot out of the thick rough before hitting it to 14 feet from where he two-putted.
McIlroy was playing in a group with Jordan Spieth and Jon Rahm, one of 11 LIV Golf players competing in the year's second major.
Spieth, bidding this week to become only the seventh man to complete the career grand slam of winning golf's four majors and first since McIlroy joined the exclusive club at the 2025 Masters, opened with a par.
Playing one group ahead is another high-profile threesome featuring 2024 PGA Championship winner Xander Schauffele, five-time major champion Brooks Koepka and LIV Golf's Tyrrell Hatton. Schauffele enjoyed a birdie-birdie start.
A further group ahead is LIV Golf's Bryson DeChambeau, who finished runner-up at the last two editions of the PGA Championship and is playing with Ludvig Aberg and Rickie Fowler. DeChambeau was one over after two holes.
World number one Scheffler, who upped his major tally to four with wins at last year's PGA Championship and British Open, is not due to tee off until 14:05 ET (18:05 CET) in the day's third-to-last group from the par-four first hole alongside Justin Rose and Matt Fitzpatrick.
Scheffler, who secured a five-stroke win at last year's PGA Championship, has runner-up finishes in his last three starts on the PGA Tour, including at the Masters, where the American fell just short of pulling off an unprecedented comeback from 12 strokes down after 36 holes.
Among the day's other later starters are Cameron Young, who is riding the wave of his best PGA Tour season to date, having already won twice this year, Shane Lowry, Tommy Fleetwood and former champions Collin Morikawa and Justin Thomas.
Stephan Jaeger was the early on-course leader after going four under through his opening six holes.