Between them, the world's top two players piled up 14 bogeys in challenging conditions at sun-drenched Merion Golf Club, Woods battling to a six-over-par 76 and McIlroy stuttering to a 75.
Though they each made an encouraging start in front of huge galleries by recording matching birdies at the par-four first, the bogeys then began to pile up as Woods fared badly with his putting and McIlroy with his accuracy.
"We both struggled today," three-times US Open champion Woods told reporters after dropping three shots before the turn and a further four on the more difficult back nine. "We both didn't get ourselves back in the tournament.
"We did what we needed to do at the first hole and got off to a nice start. He made a mistake at the second and I made a few mistakes on the front nine myself," said Woods after finishing at nine-over, a distant 10 strokes off the pace.
McIlroy, US Open champion at Congressional in 2011, hit his tee shot out-of-bounds at the par-five second hole before scrambling to a bogey that left him at three-under par.
Though he picked up one more shot at the seventh, he was undone by five bogeys on the front nine and another two after the turn as most of the players struggled to cope with tough pin positions, thick rough and narrow fairways.
"If you're not on your game 100 percent, you get on the wrong side of the greens and it's just frustrating because I didn't feel like I played too badly," said the 24-year-old Northern Irishman, who won last year's US PGA Championship.
"I missed a few shots here and there, I was trying on every shot out there and I was trying to get myself back into it, but it's tough. I was missing my woods right and my irons left, so it was a bit of a weird one today."
Woods had arrived at Merion as a heavy favourite for the year's second major after winning a season-high four times on the US Tour, but never came to grips with the pace of the subtle, contoured greens.
"I just couldn't get a feel for them, some putts were slow, some were fast and I had a tough time getting my speed right," said the American world number one, a 14-times major champion. "I didn't make anything today.
"The first two days, I had three three-putts and I was four shots off the lead, and I missed a boatload of putts within 10 feet. So I really wasn't that far off.
"If I clean up the round and don't three-putt, I'm one shot back starting out today. Basically I just didn't have the speed right this week and it certainly showed."
Asked if Merion's East Course was as penal a venue as he had ever seen at a U.S. Open, Woods replied: "Most definitely. Because of the pins, I think.
"The long holes are playing really long and short holes obviously are short, but the thing is that the pins out there, what they're giving us out there are really tough."
McIlroy finished at eight-over 218, and conceded he would need a miracle in Sunday's final round in his bid to clinch a third major title.
"It would take something unbelievable and the scores aren't that low out there," he said. "I guess, if I play well, try and get in the top 10, that would be realistic.
"I'm eight-over par for the tournament. I reckon I could get back to three or four-over par for the tournament and finish this U.S. Open on a positive note, get something out of it at least."