Also missing the weekend were No. 2 Rory McIlroy and No. 3 Jason Day, who played together for the first two rounds to disastrous results.
"This is the first time I've been in kind of the spotlight".
Four others are within three shots as the third round winds down. Brain Harman has a one-shot lead at 12 under.
Then he had a run of three birdies.
Matsuyama, the world number four, had to settle for a one-under-par 71 which left him on six under, six off the pace.
"We have come back sooner than I thought, so that's been nice really".
Joining Johnson, McIlroy, Day and Willett in going home early are a host of fellow big names.
Starting the day in a respectable position of even-par, Adam Scott sealed his exit with a disappointing 75.
The two-time major champion is 3 under for his third round at the U.S. Open and has moved into the top 25 at Erin Hills.
Koepka has only one win on the US PGA tour, at the 2015 Phoenix Open, is playing the back nine first on Saturday (NZT) and has knocked in birdies on 11, 12, 14 and 16 to be level with another American, Ricky Fowler, who led after the first round.
The cut-line for the top 60 players and fell at one-over.
Day at least managed to find one positive spin.
The performance of the 23-year-old from San Diego has been no less remarkable. You've still got to make a score.
That's something Day, the No. 3 player in the world, rarely says at a major.
Djokovic and Nadal matches postponed because of rain
I have obviously played him previous year semis here, played a really good match, played an incredible match against him in Rome. So is beating him this fortnight mission impossible? "I am not playing close to my best and everyone knows that".
Nearly an inch of rain fell on the course overnight and Reed, who beat Rory McIlroy in the opening singles at Hazeltine previous year, was one of many players to take advantage in pursuit of his first major title.
He never would have guessed it.
"It's been the best preparation going into a major, I felt like, in my career, which is playing in majors and knowing what I needed to do to prep for a tournament such as this". "And just unfortunately, this didn't pan out".
Big hitters Dustin Johnson, Rory McIlroy and Jason Day were expected to thrive on the wide open fairways of Erin Hills. If only he had hit the fairways. And even that was frustrating.
Fowler wasted no time in exploiting the conditions after teeing off on the 10th, rattling off four quick birdies to be four under.
The par-4 15th was set up as a drivable hole - downwind and only 288 yards.
McIlroy dismissed the notion of being rusty before the tournament, but conceded on his way out of Wisconsin that he hasn't played almost enough.
"At the start of the week I was thinking five-under would maybe win this thing, and I was pretty far off", he said.
"It was a surprise as I really like this golf course".
His schedule will pick up immediately. But after a blistering 7-under 65 to start the tournament, Fowler posted three straight bogeys on Nos. The top 18 players on the leaderboard going into the weekend have combined for zero majors. And instead of leaving Erin Hills fretting about how much better he could've done, he was thankful it wasn't any worse.
As he did most of the week, he hit it great - and then settled for a score that wasn't good enough.
Hideki Matsuyama had quite a day at Erin Hills. I think it's easy to lose track.
"It's going to be weird", Thomas said about the time he has to pass before teeing off on Sunday. "The execution was not there". The soft Black Course allowed players to take dead aim, and Barnes opened with rounds of 67 and 65. Unlikely as it seems, that was the last major he played on the weekend.