The British royal - who is on a visit to Jamaica - reached the finish line before Olympic sprinter Bolt, who jogged after him chuckling.
"He cheated," Bolt told BBC News. "I said we would have a rematch in London 2012 and Harry said 'I'm busy'."
Praising the prince, he added: "He's cool, very down to earth. When you meet dignitaries you think it will be difficult but he just wanted to laugh - it was an honour and a pleasure to meet him.
"I'm still the fastest man in the world, so he has a long way to go."
After the race, Prince Harry asked Bolt to sign a photo of his racehorse, named Usain Colt.
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