It gave Kaymer a battling third round of two-over 72 for eight-under 202 as the German seeks his second major title.
American pair Rickie Fowler and Erik Compton both shot best of the day three-under-par 67s to take closer order to the runaway leader.
Nobody else bettered par with testing pin positions set by officials.
2010 PGA Championship winner Kaymer had started the third round with a six stroke lead after reaching halfway with a record 10-under total of 130 at Pinehurst No.2.
Behind Fowler and Compton it was Swede Henrik Stenson and Dustin Johnson, who both carded level-par 70s, to stand two-under 208 and maintain slim hopes of lifting the trophy.
Kaymer, bidding to become the first man to win the Players Championship and the U.S. Open in the same year, recovered from two early bogeys by eagling the par-5 fifth hole.
But missing fairways, he made three bogeys to come back toward the pack until holing from eight foot on the last for a morale-boosting birdie.
“It was good. I didn’t play as well as the first two days, but I kept it together,” Kaymer told the PGA Tour website.
“The USGA put the pins in very, very difficult positions.”
Behind the leaders, Phil Mickelson’s hopes of completing a career grand slam ended with a two-over 72 for five over.
“If I hit it better and make some putts, I think I can shoot four or five under par, end around even, finish second again,” he joked in a reference to his six runner-up spots in the only major to elude him.
Defending champion Justin Rose of England moved into a tie for 10th, with rising star Jordan Spieth also on that mark, after a fine level-par 70 for one-over 211, but still nine shots behind Kaymer.