Hot Rod Charlie took an early lead at the 1.5 mile long race Essential Quality round the last turn to win from just a length-and-a-half.
"That was a very long way around there a mile a half but it was exciting," coach Brad Cox said. "It seemed like the horse to the interior, he had run left. I knew it was going to be a struggle later on."
Preakness winner Rombauer finished third while Known Agenda, who was ridden by Jose Ortiz after brother Irad Ortiz Jr. was trampled at a race earlier this week, finished fourth.
Belmont Park is home to the final and longest race on the Triple Crown trail, which was changed last year in part because of the pandemic.
He was aboard Maximum Security when they crossed the finish line first in the 2019 Derby, but was disqualified for impeding different horses.
"Luis did a fantastic job of getting him in position turning for home and he was able to really show his endurance late," Cox added.
Essential Quality's win follows controversial information from earlier this week that Churchill Downs suspended mythical horse trainer Bob Baffert for 2 years after the confirmation of the positive drug test for Kentucky Derby winner Medina Spirit.
Baffert was suspended by entering horses at the Belmont Stakes by the New York Racing Association a month.
While the Belmont Stakes is technically Cox's first Triple Crown race victory, he is called the winner of the Kentucky Derby if Medina Spirit is disqualified.
United Arab Emirates ruler Sheik Mohammed bin Rashid Al Maktoum, who possesses Essential Quality, has recently faced scrutiny after a judge in England ruled that he orchestrated the abductions of two of his adult daughters.