Behind the green in two shots at the par-four 18th, the Englishman was attempting to chip from 20 feet away but, as he addressed his ball, he felt the ground underneath give way.
After backing off, Rose was convinced the ball had not oscillated but subsequent television replays confirmed that there had been a slight move - a "quarter of a dimple," according to Rose - toward the toe of his sand wedge.
His one-under-par 71 was subsequently adjusted to a 73 and he will go into Sunday's final round at the TPC sawgrass on five-under 211, seven strokes behind co-leaders Martin Kaymer of Germany and American Jordan Spieth.
"That was a bitter pill to swallow at the end of a battling day," Rose told reporters after his presumed par at the last had been amended to a double-bogey six. "In some ways, it is my own fault for trying to be my own rules official.
"I hit it through the back of 18 and as I soled my club, there's some really abnormal ground conditions there and I was expecting to have a fairway lie and put my club down.
"And it was a very, incredibly spongy, thatchy, bit of fairway and the whole sort of surface underneath my wedge gave way. And at that point you make a call. Did my ball move? Did it just sort of move with the turf and oscillate?"
Both Rose and his playing partner, Sergio Garcia of Spain, looked up at a replay on a giant television screen behind the 18th green and agreed there had been no ball movement.
However, officials later reviewed the incident on video in the television compound and Rose was given one stroke penalty for his ball moving at address and a further stroke for not replacing the ball after it had moved.
"Under 50 times magnification in the truck, maybe the ball moved a quarter of a dimple toward the toe of the club and obviously, if the ball moved, it moved and I get assessed an extra stroke penalty," said Rose.
"Whereas if, in the moment, I would have called the rules official, I would have only been assessed one stroke by moving it back. But as a player you have to make that judgment call.
"It's disappointing. I've gone from trying to chip in to make three to walking off with six. At least the right decision's been made. The ball moved. I made a mistake. It's not a one-stroke penalty, it's two. I got to just move on tomorrow."
- Sports & Recreation