The American signed for an even-par 70 around the pristine Shinnecock Hills on Saturday, enough for a six-shot lead over a chasing pack of Sam Stevens, Tom Kim, Sahith Theegala and the big fish Scottie Scheffler.
Key to Clark's round was four critical par saves over five holes on the back nine, which included a tricky 15-footer on the 13th. He slipped back with a bogey on the 15th, but then came the magic. Clark crunched a majestic 3-wood to four feet on the par five 16th that set up the only eagle all week.
He closed with a bogey at the last, but the damage had been done.
"Really one of the shots of the tournament," Clark said of his 275-yard high cut into the 16th green.
Meanwhile, Scheffler, who usually saves his best for last, carded a one under 69 to give himself an outside chance on Sunday.
"We've been battling hard for a few days, and I did a good job of keeping myself in the tournament," said the 30-year-old.
"I'll need a really nice round tomorrow if I'm going to try and catch Wyndham."
Stevens closed within two shots of Clark on the front, started the back nine with three straight bogeys and closed with six straight pars for a 72. Kim dropped two shots for his 72 and Theegala had one birdie, one bogey and 16 pars for a 70.
"It's all in Wyndham's hands, really," said Xander Schauffele, who is seven shots behind.
"If he plays a really solid round of golf tomorrow - if he shoots even par or one over or two over - he's going to win the golf tournaments. That's how I think it's going to pan out."