The cut for the top 60 and ties was at 1-over 145, tying a U.S. Open record set in 1990 at Medinah.
Harman closed with two birdies and three tough pars for a 5-under 67 that gave him a one-shot lead at 12-under 204.
Both players - ranked No. 2 and No. 3 in the world, respectively - put themselves in poor position with bloated opening-round scores: Day a 7-over 79 and McIlroy a 78.
Johnson, who had bullishly expected to do well on a course he believed to be perfectly suited to his game, admitted he was surprised to be out after only 36 holes.
"I played very well today, and I felt very comfortable", Fleetwood said. I think the more rounds I can play, I'm hopefully going to get rid of all that stuff and hopefully strip it down to what you saw the last six holes.
The soft, forgiving conditions created opportunity for major movement up the leaderboard for those players willing to take it.
On another day of low-scoring at the Erin Hills course in Wisconsin, Casey and compatriot Tommy Fleetwood were bunched on seven under alongside Americans Brooks Koepka and Brian Harman after the second round.
Behind the leading quartet, a logjam grouped eight players within two shots of the lead.
"Usually when you shoot even in a U.S. Open and you're one off the lead, you're not six down afterward", J.B. Holmes said.
Also at 5 under was Si Woo Kim (70), Xander Schauffele (73), amateur Cameron Champ (69) and Brandt Snedeker (69).
Chez Reavie matched Matsuyama's 65 in round two to lead a group at four under. "So you've got to minimize those mistakes, minimize those bogies".
Rain-softened conditions at Erin Hills made greens more receptive and a lack of brisk winds left the course virtually defenceless.
In fact, you have to go down to 19th place to find a victor of a major, Sergio Garcia and Martin Kaymer, at three under.
Fleetwood loved the way he salvaged a bogey from the mess he was making at the last hole of the day.
"It would change my life, I know that", he said. "It was a bit of a roller coaster".
But while Casey was relieved after his gutsy fightback, it was back at the drawing board for McIlroy and Day after their disappointing exits. "It means I have a lot better chance to win the tournament than I did when the day started", said Thomas after becoming the 29th player to shoot 63 in a major championship.
"This is my first time in contention in a major, so whatever happens I'll be doing my best and seeing how well I can finish", he said. Stricker, who played in the morning, wasn't 100 percent sure he would make the cut after his even-par 72 left him at 1-over for the tournament, though all signs pointed to him advancing to the weekend.
McIlroy, as well as Day, will play the Travelers Championship near Hartford, Conn., next week as he gears up for the British Open.
McIlroy meanwhile said a new putter being used for the tournament was not the problem. I got off to a pretty good start, which I really haven't done yet, so that was nice. "It's just a matter of getting competitive rounds under my belt".
"It's just golf. It's frustrating". He went from pouring putts into the center of the cup to burning the edges, and his 39 on the back nine cost him the lead, though not his chances of breaking through for that first major.