Jockey Irad Ortiz produced the 16-1 shot with a thrilling late surge to get up by a nose after the one and a half mile race -- the third leg of the Triple Crown.
The connections of both horses faced an anxious wait before the winner was declared of the $1.5 million classic.
"I was glad to see them put that number (No 13) up," said winning trainer Steve Asmussen, whose other runner Gettsburg had set a strong early pace.
Creator, winner of the Arkansas Derby, had flopped in the Kentucky Derby, well adrift of winner Nyquist, but showed his true worth over the longer trip.
The Preakness winner did line up, starting as 7-5 favorite, but faded to finish 11th, beaten by 14 lengths.
Japanese -based colt Lani, ridden by Yutaka Take, finished third, one and a half lengths adrift of the first two.
It was only the fourth time that the Belmont had been decided by the closest of the margins as Creator won his third race from 10 starts and took his career earnings past $1.5 million.
Asmussen praised Ortiz for his part in the narrowest of wins.
"I thought Irad gave him a perfect trip. I thought he saved yards and won by inches. He made the difference," Asmussen told the official Belmont Stakes website.
Nyquist's poor showing at the Preakness -- hit by a fever -- meant there was to be no repeat of the 2015 heroics of American Pharoah, only the 12th horse in history to win the Triple Crown and the first for 37 years.
But the battle between the two grays, both coming off poor runs in the Kentucky Derby, provided a compelling storyline.