At a simple funeral ceremony in the Czech capital's 19th-century national theatre, politicians, diplomats and sporting personalities from around the world paid tribute to the four-times gold medal winner.
He died on 21 November, aged 78.
Zatopek's coffin was draped with the Czech flag, with the Olympic flag hanging overhead.
His widow Dana Zatopkova, herself an Olympic gold medallist in Helsinki in the javelin, requested that Zatopek not be given a state funeral.
International Olympic Committee president Juan Antonio Samaranch awarded Zatopek posthumously the Pierre de Coubertin medal, the IOC's highest honour.
"I was in the Olympic stadium in Helsinki in 1952 when he was the winner of the marathon," he said.
"All 60,000 spectators were standing and crying Zatopek, Zatopek, Zatopek. At that moment, I understood very well what the Olympic spirit means.
"Emil was a living legend for all generations. Emil Zatopek was a legend, and a legend never dies."
Inspiration
International Amateur Athletics Federation president Lamine Diack awarded Zatopek the IAAF's Golden Order of Merit, "for how he inspired the whole world".
At the Helsinki Games in 1952 Zatopek swept to victory in the 5,000 and 10,000 metres, and the marathon within the space of eight days, each in Olympic record time.
It was the first time he had run the 26-mile marathon.
Four years earlier, he had won a 10,000 metres gold medal and a silver in the 5,000 metres at the London Olympics.