He had 310 yards to the hole when he hit 3-wood that could have led to big trouble if he went too far long or left. Jason Day and Rory McIlroy also missed the cut, and this marked the first time the top three players in the world have all missed the cut in a major.
For the first time since the two golfers started playing in majors, the weekend at the U.S. Open will be without a McIlroy and a Day.
However, plenty of others were firmly in contention at the start of the penultimate day; only eight shots separated the leaders from those who made the cut on the bubble.
"It was a surprise as I really like this golf course".
Another warm, dry day is drying out the course during the second round of the U.S. Open, and the players are noticing a difference.
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. And it's especially hard to win a first major when you're the rabbit, setting the pace for the opening two days.
Rickie Fowler failed to capitalize on the great conditions, shooting a 73 that kept him on the first page of the leaderboard but left him in a three-way tie for second place with Jamie Lovemark and JB Holmes.
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Thomas says "I had no idea in terms of 9 under being the best in the U.S. Open". "There were a couple of dicey pin placements out there that you had to be careful about, but it was still scoreable". "I think the more rounds I can play, I'm hopefully going to get rid of all that stuff and hopefully stripe it down to what you saw the last six holes". The claw grip has been working for him on the greens.
Following a mini-meltdown on his front nine, where he dropped five shots in four holes, including an 8 on the par-five 14th, the Englishman bounced back with five birdies in a row. He birdied four of his last six holes - he missed two birdie putts of 10 feet and two-putted for birdie on the par-5 seventh - to rally for a 71.
Day carded a three-over-par 75, leaving him 10-over, while Scott shot a 75 to sit at three-over. "Part of that is just age and part I'll give credit to Johnny McLaren (his caddie), credit to my wife and my little boy".
"The majors have a different feel and sound to the roars and to hear the crowd go insane when I holed that putt on 18 was really cool", said Thomas, whose back-to-back wins in Hawaii in January included an opening 59 in the Sony Open.
McIlroy's pre-tournament comments proved disappointingly accurate after he had predicted that anyone who could not hit the wide fairways " might as well pack your bags and go home".
In the final round at Oakmont a year ago, his golf ball moved slightly as he positioned himself for a short putt on the fifth hole.
"Oh gosh, Jimmy, be good", he said to caddie Jimmy Johnson when the ball was in the air, and it was close to ideal. Obviously, I'm not here on the weekend, so it's unfortunate. It's just a matter of getting competitive rounds under my belt. It was wonderful to see that there was, I felt, no knee-jerk reaction to yesterday's scores.