He had a six-shot lead at the turn but hit only three fairways on the nine and missed a 4-foot par putt on the 18th for a 70. He dedicated his first victory, the 2013 Johnnie Walker Championship, to his dog, Maisy.
Late last year, the 24-year-old from Louisville embarked on the best stretch of golf in his young career.
Hideki Matsuyama is second at 12 under. He is listed at 5-foot-7, 150 pounds.
Harman also bogeyed No. 13 to drop back to 11 under.
"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.
Scottie Scheffler is the low amateur for this year's U.S. Open.
Fowler, who shared the 36-hole lead at the Masters in April, never came seriously close to bogey because he was never in trouble. Vijay Singh was the last player to accomplish the feat in 2003 at Olympia Fields.
Fowler was among those who wouldn't mind seeing the conditions toughen up for the final 18 holes.
Harman, bidding to become the first left-hander to win a US Open, is a victor on the PGA Tour this year while Thomas is the world number 13, a three-time victor this season and a member of the exclusive "59" club after breaking 60 at the Sony Open this year.
Rickie Fowler, who seemed to have lost some momentum on his back nine Friday, came back today with a four-under 68. Mickelson has won every major but the U.S. Open.
As for scoring drama - well, this was one time he may have wished he didn't know where he stood. 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.
The Front 9 has the easiest Holes and with the conditions they way they were, everyone was making Birdies on them. Fowler finished the day -11 Tied for 2nd.
CARRY MY BAG, PLEASE: Jimmy Johnson has now carried the bag for two players to shoot 63 in a major: Thomas on Saturday, and Steve Stricker at the 2011 PGA.
It was only a year ago at Oakmont that Andrew Landry, who had to make it through two stages of qualifying to get into his first U.S. Open, shared the 36-hole lead with Dustin Johnson.
Brooks Koepka is trying for his first major title, and he is off to a solid start in the final round of the U.S. Open.
Golf: Matsuyama joins Aoki as major runner-up from Japan
"Then he went on to (WGC) Mexico and holed that monster putt from about 80 feet on the last green, which took him into second on his own, won him a cheque of almost a million dollars and propelled him right up the Order of Merit and world rankings".
Oosthuizen, whose sole major title to date came at St Andrews in 2010, birdied the first, fourth, seventh and eighth to move to four under par, while 2015 victor Spieth had covered his first 11 holes in level par. The soft Black Course allowed players to take dead aim, and Barnes opened with rounds of 67 and 65. Some brilliant players have a lot of ground to make up but I fancy they'll struggle.
Spieth opened with a birdie on No. 1 and said to his caddie, "Fifteen more". Two down, 14 to go.
He then drilled a 300-yard second shot to around eight feet before rolling in his eagle putt to roars from the galleries at the Erin Hills Course in Wisconsin.
As Fleetwood surprisingly wobbled and Thomas took plaudits, Brian Harman proved the merits of the quiet man. He shot 81 the next day in a blustery wind. He tees off later on Sunday.
Thomas's 63 was remarkable given what might have been; he dropped shots on the 4th and 10th, before passing up a relatively simple eagle chance on the 15th.
A three-time victor on the PGA Tour this season, Thomas also joined the exclusive "59" club by breaking 60 at the Sony Open, but he may have saved his best for Father's Day weekend and his quest for his first major crown.
Johnson put his weekend in jeopardy after missing a 6-footer for par on the par-3 13th. He would two-putt for birdie, and he wasn't done producing highlights.
The world's fifth-ranked player is well off the lead. But I'm looking forward to getting the job done.
The Victorian shot a disappointing even-par 72 to stay at four under, sharing 17th.
"Being this soft, birdies are going to happen". Even though it will be hard, I don't anticipate this being a blood-letting. Then there was Tommy Fleetwood who was all over the Green.
It's the most players tied after 36 holes of the USA since 1974 at Winged Foot, only the names from 43 years ago resonate more than today Raymond Floyd, Hale Irwin, Gary Player and Arnold Palmer.
The wind is gusting up to 25 miles per hour with the forecast calling for it to go as high as 30 miles per hour in the afternoon when the leaders tee off.
But that's not all that makes the possibilities so limitless Saturday. There were five birdies and two bogeys in a round that provided a timely reminder of the 23-year-old's class.
Nobody in the top 16 on the leaderboard has won a major.
Logjam At Top of US Open Leaderboard After Round 2
And if that's not enough of a traffic jam at the top, 18 players are separated by three shots to start the third round. Not bad for a guy who made the cut on the number. "So if I get through to the weekend, I can slowly inch my way back".
Trump Admin Decides to Allow 'Dreamers' to Stay in US (For Now)
But Thursday's decision said that another Obama-era program, the Deferred Action for Parents of Americans, will be formally ended. While the Trump administration is permitting DREAMers to stay in the country for now, their long-term status remains unclear.
Trump will clamp down on Cuban travel, trade
However, traveling to Cuba in the future is expected to again become more hard under changes imposed by the Trump administration. The expected directive Friday instructs the Treasury and Commerce Departments to establish new rules within three months.