Fowler's early exit from the event came after a wayward tee shot at the par-four sixth hole that appeared to strike a palm tree and remain nestled in one of the fronds at TPC Sawgrass.
The ball was clearly visible, but though spectators vowed it was Fowler's, he could not identify it with 100 percent certainly, even with binoculars.
After a discussion with rules official Mark Russell, Fowler declared a lost ball and had no choice but to return to the tee for his third shot.
He double-bogeyed the hole and, perhaps shaken by the incident, also dropped two shots at the next on his way to a 71 for one-over 145, destined to miss the cut by a couple of shots.
"Obviously didn't make a great swing, but it's five yards right of the fairway and the marshals and fans were standing right there, saw it was the tree it hit and obviously got stuck up there," Fowler said.
"Unfortunately, the part of the ball that was showing was just all the white and dimples. I couldn't see any of my markings and so couldn't identify it, so back to the tee."
Fowler, the 2015 champion, lamented that under the rules of golf a ball does not have to be identified if it apparently goes into a hazard, a marked area of the course that contains a difficult obstacle.
Had the palm been in a hazard, the American could have taken a one-stroke penalty and dropped nearby, instead of having to return to the tee.
"It was pretty clear that the ball was there," he said.
(Reporting by Andrew Both; Editing by Toby Davis)
