Union Rags, patiently ridden by John Velazquez, won the $1 million Belmont Stakes on Saturday with a late burst up the rails.
Paynter, who led until the final few strides, held on to finish second, a neck behind Union Rags, while outsider Atigun was third in the final leg of U.S. thoroughbred racing's Triple Crown.
The Triple Crown was not up for grabs after I'll Have Another, which won the Kentucky Derby and the Preakness Stakes in brilliant fashion, was scratched on the eve of the race after suffering a leg injury.
Union Rags was one of the favourites for the Kentucky Derby in May but could only manage seventh after a troubled run.
His connections switched jockeys and decided to skip the Preakness to save him for the 1-1/2 mile (2,414 metres) Belmont, the longest and most gruelling of the three classic races.