Rain-softened conditions at Erin Hills made greens more receptive and a lack of brisk winds left the course virtually defenceless.
Four players are tied for the lead at the U.S. Open after Friday's second round.
The 24-year-old Thomas eagled the par-5 18th for just the fifth 63 in U.S. Open history.
"I feel like I'm striking it very well". Many were headed to the airport.
Johnson's exit came after world number two Rory McIlroy and world number three Jason Day also missed the cut after disappointing rounds. He had no explanation or theory on why the top three players in the world would not be around for the weekend - the first time since the Official World Golf Ranking debuted in 1986 that the top three in the world missed the cut at a major.
Justin Thomas joined a logjam at the top of the US Open leaderboard on Saturday (June 17), rattling off six birdies and a bogey in his opening nine holes to grab a share of the lead as the third round got under way.
Nearly an inch of rain fell on the course overnight and Reed, who beat Rory McIlroy in the opening singles at Hazeltine a year ago, was one of many players to take advantage in pursuit of his first major title.
Also at 11 under was Tommy Fleetwood, who was poised to take the lead until his pitch came up short, his next shot went 60 feet down a slope on the back of the 18th green and he turned potential birdie into bogey and settled for a 68.
Jun 16, 2017; Erin, WI, USA; Rory McIlroy walks off the 18th green during the second round of the U.S. Open golf tournament at Erin Hills.
"I hate just being in the situation where I've been in a good spot and maybe let it get away from me a little bit and let some mistakes compound and turn a round that you (just) kind of fight through it and end up being in a decent spot after the day", Fowler said. "We're simply not going to cross that line into politics", Mike Davis, executive director of the USGA, said in May. "I really like this golf course", Johnson insisted.
"I think this week the scores have been low because the weather has been so good". That should have affected everyone the same way, but it was particularly troublesome for the field's elite players.
Overnight leader Rickie Fowler had people watching on the edge of their seats on Friday, but appeared to play far too conservatively.
Thomas's pyrotechnics were the main event on a day filled with thrilling shots and wild scoring swings.
Fleetwood, 26, ended a four-year wait for his second European tour win with a dazzling victory at the Abu Dhabi Championship earlier this year, when he held off a late surge from world No 1 Dustin Johnson.
With the entire field separated by just eight shots after the cut fell at one over, 2015 victor Jordan Spieth had hoped to get himself into contention but struggled to a 76.
Johnson insisted he was happy with his long game at Erin Hills, but he could not back up his ball striking with his putting as he failed to build on a positive start to his second round.
McIlroy has played in only seven tournaments this season and was coming off a layoff resulting from a nagging rib injury. With four par-5s and wider-than-usual fairways, some thought the tournament would be a bomber's paradise. "Some of it nearly takes the bombers out of it". Neither could recover to make the cut Friday, as McIlroy shot 71 to finish at 5-over and Day shot 75 and finished 10-over. Not everyone can take advantage.
Not that anyone is complaining about the course.
"Even though it's very disappointing to not be here on the weekend, I think these last two rounds will serve me well going into the summer, " he said.
That's something Day, the No. 3 player in the world, rarely says at a major.
"You get going in that hay, and you can't get out of it".
And on the leaderboard.
Not to be overlooked was Si Woo Kim, who captured The Players Championship last month. The leaderboard is shaping up quite nicely. "I did the work, looked at the golf course, made sure that I could actually play and visualize the golf course", he said.