Essential Quality won the Belmont Stakes on Saturday, beating second-place Hot Rod Charlie and third-place Rombauer for the win.
Luis Saez was the jockey; Brad Cox the trainer.
Saez dedicated his win to brother Juan Saez, who died in 2014 in a riding accident.
"This was the race that I wanted to win," Saez said. "Today we made history."
It was Cox's first Triple Crown win. Another horse he trains, Mandaloun, came in second place at the Kentucky Derby and could earn Cox another Triple Crown win following controversy over first-place finisher Medina Spirit.
The owner of Essential Quality, who was the Derby favorite, is United Arab Emirates Prime Minister Sheikh Mohammed bin Rashid Al-Maktoum.
Lawyer Lisa Bloom alleged in a tweet before the Derby that he was holding his adult daughters against their will. The sheikh and the UAE deny the allegation. In late May, images of one of the daughters appeared on Instagram.
Godolphin LLC, a thoroughbred breeding operation founded by the prime minister, did not immediately return an emailed request for comment Saturday.
The Triple Crown horse racing triumvirate celebrated its return to normal this year with the running of its final leg Saturday just outside New York City.
But normal came with an asterisk, as the sport's most successful living trainer, Bob Baffert, was suspended from Saturday's race.
Baffert called the positive test "the biggest gut punch in racing for something I didn't do," but later said Medina Spirit had been treated for dermatitis with a topical ointment called Otomax, which contains betamethasone.
Medina Spirit and two other Baffert-trained horses were allowed to run the second leg of the Triple Crown, the Preakness, May 15, after passing three rounds of drug tests.
On Wednesday, however, Churchill Downs, home of the Derby, suspended Baffert for two years following confirmation of Medina Spirit's positive drug test. The suspension threatens the horse's 2021 Derby win.
Bay colt Rombauer won the Preakness, and there was no chance of a single Triple Crown winner this year.