The 24-1 long-shot Gronkowski battled from the back of the pack to cross the line second, almost two lengths behind Justify, while the 5-1 Hofburg finished third amid overcast but dry conditions.
The victory marks the second Triple Crown win for Hall of Fame trainer Bob Baffert, who also won the Kentucky Derby, Preakness Stakes and Belmont Stakes with American Pharoah in 2015.
"This never gets old," an emotional Baffert said after the race.
"American Pharoah, he'll always be my first love. For this horse to do it for (jockey) Mike Smith, he deserved something like this. It feels pretty good."
Baffert said Justify was simply the best horse at the track on Saturday.
"He could have won every race on the undercard today, he's just that kind of horse."
The large and muscular Justify, owned by China Horse Club, Head of Plains Partners, Starlight Racing & WinStar Farm, made 52-year-old Smith the oldest jockey to ever win the Triple Crown.
"This horse ran a tremendous race. He's so gifted he’s sent from heaven," Smith said of Justify, who was the 4/5 favourite.
"He's just brilliant."
Smith thanked Baffert for giving him the opportunity to ride Justify into the history books.
"He's made a lot of my goals come true but today, he made my dream come true. I appreciate it."
Justify was sired by Champagne Stakes and Florida Derby champion Scat Daddy and was born at Glenwood Farm in Versailles, Kentucky.
From early on, Baffert said it was clear that Justify was special.
"I've wanted to see that horse's name up there because we knew he was brilliant from day one."
With the win, Justify, who did not race as a two-year-old, improved to 6-0 in his young career, which started just 111 days ago.
Some had wondered whether the colt might show signs of fatigue following a busy schedule but that was not the case as he broke from his number one post position and was never seriously challenged by any of the other nine horses.
Saturday's race, the 150th running of the Belmont Stakes, marked the fifth time Baffert came to Belmont with a shot at the Triple Crown.
(Reporting by Rory Carroll; Additional reporting by Andrew Both; editing by Clare Fallon / Ian Ransom)
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