Paynter led for much of the race, but ended up in second after jockey John Velazquez led Union Rags on a late charge. Atigun came in third.
The end of his racing career became all the more official Saturday when, minutes before the Belmont Stakes contenders broke from the gates, he was led to the winner's circle and ceremoniously retired.
"We felt that this would be a fitting ceremonial retirement for an incredible racehorse," trainer Doug O'Neill said before the ceremony. "There are many fans who traveled from near and far to see I'll Have Another today, and we wanted to give them a chance to help us send him off to retirement."
The horse's owner, J. Paul Reddam, announced Friday that I'll Have Another would be retired one day before he would have attempted to become racing's 12th horse to win the Kentucky Derby, Preakness and Belmont Stakes, a triumph known as the Triple Crown.
Jockey Mario Gutierrez, born in Mexico, described the "unbelievable journey" he has been on -- rocketing from relative obscurity racing in western Canada to international fame in his first two Triple Crown contests -- thanks to I'll Have Another. The jockey expressed faith that the horse, had he been healthy, would have made history Saturday.
"A lot of people didn't believe in him since (the) Santa Anita Derby, the Kentucky Derby, (opining that) everything was going to be a huge deal for him. And he proved them wrong," Gutierrez told reporters Saturday. "I know if he was 100% today, he would prove everybody wrong again."
Affirmed was the last horse to win the Triple Crown, in 1978. Since 1990, only seven horses have won the first two legs.
The Belmont is considered to be the longest and most grueling of the three Triple Crown races. The horses run one complete lap over 1½ miles. The Derby is 1¼ miles, and the Preakness is 1 and 3/16 miles.
The Triple Crown did not acquire its name until Sir Barton won all three races in 1919. Just 11 horses have won the prestigious honor, most recently in 1978, when Affirmed grabbed the title.
Only two other Derby and Preakness winners were unable to run in the final leg of the Triple Crown: Burgoo King in 1932 and Bold Venture in 1936.
Three decades stand out as having multiple Triple Crown winners: the 1930s with three winners, the 1940s with four and the 1970s with three, most notably Secretariat in 1973.
Secretariat also set the world record in 1973, winning the Belmont Stakes by 31 lengths and running the course in 2 minutes, 24 seconds.
Since the 1970s, a few horses have come close to winning the Triple Crown. In 2004, the largest crowd in New York Racing history, 120,139 people, attended the Belmont to see Smarty Jones attempt the 12th Triple Crown win. Smarty Jones finished second. In 2003, favored Funny Cide finished third in his attempt. Most recently, Big Brown's Triple Crown hopes were dashed in 2008.