Overnight leader Fowler led playing partner Clark by two as they stood on the 18th tee at Los Angeles Country Club.
Clark had just dropped a shot at the 17th, but fired his approach at the flag at 18 and made a six-foot birdie putt.
Fowler, who had gone 12 holes without a bogey as a string of rivals faltered on the treacherous back nine, saw his 42-foot birdie putt skim the edge — but his par putt from inside four feet coming back lipped out.
“You could see from the first putt, there’s a lot of slope there,” Fowler said. “I’m not sure why it didn’t move. It should have. I hit a good putt, so really can’t go back on it.
“It would be nice for that one to go in. Really doesn’t matter, having the lead, being one back, two back. You’re going to have to play good golf tomorrow.”
Fowler signed for an even par 70 while Clark posted a one-under 69 that left them one in front of Northern Ireland star McIlroy, who carded a 69 for 201 to remain in position to claim a fifth career major and his first since 2014.
World number one Scottie Scheffler was alone in fourth on 203.
After two days of record scoring, the sun-baked LA Country Club North Course — hosting the championship for the first time — proved plenty capable of providing a classic US Open test of patience and nerve.
Fowler, who had a stunning 18 birdies over the first two rounds, couldn’t match those fireworks, his three birdies including a 36-foot putt at the seventh and a 70-footer from off the green at 13.
Clark, a long-hitter who broke through for his first US PGA Tour title at Quail Hollow last month, had grabbed a one-shot edge through nine holes before back-to-back bogeys at the 11th and 12th.
Unable to get up and down from a greenside bunker at the par-three 11th, Clark then botched his first attempt to chip out of greenside rough at the 12th.
He rebounded with a birdie at 13, but it looked as if he’d be chasing on Sunday after his second shot at 17 found the barranca right of the green and he took a penalty drop on the way to bogey.
Limiting the damage was “huge,” Clark said, as was the birdie at 18.
“I wanted to be in the final group,” Clark said. “I’m not a huge scoreboard watcher, but walking up there I kind of knew where we were at. I really wanted to be in that final group.”
McIlroy had three birdies and two bogeys and was rarely in real trouble.
“The golf course definitely got a little bit trickier today than the first couple of days,” McIlroy said. “Felt like I played really smart, solid golf.
“Hit a lot of fairways, hit a lot of greens. Sort of felt somewhat stress-free out there, if you can ever call golf at a US Open stress-free.”
Scheffler, the 2022 Masters champion who started the day five adrift, picked up three strokes in the last two holes.
Coming off his fourth bogey of the day at the 16th, Scheffler holed out from 196 yards in the fairway for eagle at the 17th, where there were only four birdies all day.
He then drilled a 22-foot birdie putt at the last.
“Today it seemed like every time I got off line I was really fighting for par — just fortunate to see that shot go in on 17 and then a nice birdie on 18 to kind of get myself back into it,” Scheffler said.
Scheffler was one stroke in front of fellow American Harris English, who was one off the lead after his fourth birdie of the day at the 10th but had four bogeys the rest of the way in a one-over 71.
Two-time major winner Dustin Johnson and 2021 Olympic champion Xander Schauffele shared sixth on five-under 205, one shot in front of Japanese qualifier Ryutaro Nagano, who had an eagle in his 68.
It was a further stroke back to reigning British Open champion Cameron Smith of Australia, former US Open champion Bryson DeChambeau and South Korean Tom Kim on 207.
Kim fired seven birdies in the first 10 holes to reach six-under for the tournament.
His front-nine 29 tied the US Open nine-hole scoring mark, but he had three bogeys coming in on the way to a four-under par 66.
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