McIlroy at least improved his position in round two, nearly holing his tee shot at his final hole - the par-three ninth - as he completed a 71 with four late birdies.
The last six majors have crowned first-time champions and that trend looks poised to continue at Erin Hills where you have to look way down the leaderboard to 19th before finding a major victor in U.S. Masters champion Sergio Garcia of Spain.
World number one Johnson becomes the ninth player to miss the cut having won the USGA's blue ribbon event 12 months previous.
The top three players in the world have never missed the cut in the same major dating to when the world ranking began in 1986.
"I know it's cliche, but the last thing you need to be doing is thinking ahead, especially on this golf course". This week marked his seventh U.S. Open; he'd never missed a cut, and counts five top-10 finishes.
With Johnson, McIlroy and Day misfiring, it was left to a clutch of unheralded players to dominate the upper reaches of the leaderboard.
But Koepka was even better, carding four birdies on his bogey-free outward nine as both players settled in at nine-under with nine to play.
United States considers sanctions on North Korea trade allies
North Korea repatriated a sick USA citizen it had held captive for 17 months, and Dennis Rodman arrived with fanfare in Pyongyang. Mr Rodman is a friend of North Korean leader Kim Jong-un and has made several visits to the country in recent years.
Tall fescue grass on the fourth, 12th, 14th and 18th holes at Erin Hills was being cut on Tuesday as McIlroy spoke to the media, which caught the 2011 champion by surprise.
PGA Tour rookie Xander Schauffele and veteran Brit Paul Casey closed to within one of Fowler, adding drama late in the day.
"I had been swinging it well and it felt really, really good a couple holes later to be picking the ball out of the hole for a birdie".
"We're in a good spot", Fowler said, referring to his status in the first-person plural after shooting 1-over 73.
Then came the par five 14 hole. So there's a very good chance this weekend that the run of first-time major winners dating to the 2015 PGA (Jason Day) will extend to seven.
No left-hander has won the U.S. Open, the only major championship without a left-handed victor.
Meanwhile, Graeme McDowell is also in the midst of his second round and is now one shot clear of Dunne on 3-over but also sitting outside the cut mark.
Rory McIlroy joked earlier in the week that anyone who could not hit such wide fairways "might as well pack your bags and go home". Obviously, I'm not here on the weekend, so it's unfortunate. "I guess it's rare you get through a U.S. Open or any major without some kind of hiccup".
"It's just golf. It's frustrating but I don't let it bother me". Unlikely as it seems, that was the last major he played on the weekend. "I couldn't possibly shoot any higher than I did". But he also struggled around the greens, failing to get up and down once in six opportunities.