After leading for much of the race, Funny Cide fell behind Empire Maker on the final stretch of the muddy, rain-soaked race. He was also passed by Ten Most Wanted, who finished second.
Funny Cide was looking to become the first New York-bred thoroughbred to win the Triple Crown. He finished third.
Empire Maker was the favourite to win the Kentucky Derby in May but finished second behind Funny Cide, who went on to win the Preakness Stakes two weeks later.
Empire Maker, right, with jockey Jerry Bailey up, crosses the finish line to win the Belmont Stakes. (AP Photo/Roberto Borea)
Despite heavy rains at Belmont Park in Elmont, N.Y., a large crowd turned up hoping to see history made.
Instead, they witnessed the fifth Derby-Preakness winner in the last seven years to come up short in the 1 1/2-mile Belmont, the longest and most gruelling of the Triple Crown races.
The last horse to win the Triple Crown was Affirmed in 1978
Empire Maker, owned by Saudi prince Khalid Abdullah, bruised his foot Derby week and finished 1 3/4 lengths behind Funny Cide. He skipped the Preakness, but was "dead fit" for Belmont, said trainer trainer Bobby Frankel.
"You know he's the best horse," Brooklyn-born Frankel said. "He pulled up but then he took off when that other horse (Ten Most Wanted) challenged. I wanted the race to shape up like that."
With the victory, jockey Jerry Bailey captured the Belmont for the second time in 18 attempts, winning his first aboard Hansel in 1991.
Empire Maker took the 135th Belmont Stakes in a time of 2:28.26.
with files from the Associated Press