Clashes broke out between his supporters who were apparently competing for space to view the ceremony.
Onlookers tossed flowers as a military jeep carrying Peron's wooden coffin draped in the Argentine flag made its way through downtown Buenos Aires in a journey marked by several outbreaks of violence from his followers.
The relocation marked a new chapter in a saga involving Peron's corpse, which has been disinterred, mutilated by thieves who sawed off his hands, and was the focus of a lengthy battle by a woman claiming to be his illegitimate daughter.
Shouts of "Viva Peron!" rang out as a motorcade carrying the remains of the leader, who was married to "Evita", stopped at the headquarters of the country's biggest labour union en route to a new US$1.3 million (A$1.7 million) mausoleum built to house his remains.
The burial will see Peron laid to rest in the Buenos Aires suburb of San Vicente on the grounds of what was once his weekend retreat.
Worried about feverish support among his followers, Argentina's military leaders ordered Peron's coffin removed in the 1970s from the presidential grounds and banished to his family's more modest crypt.
Officials have said they wanted to relocate his remains to a location they say is more befitting one of the country's leading figures.
"I hope we see another patriot like him one day," said Americo Armada, 75, as he waited for a glimpse of Peron's coffin.
Supporters clash
Fighting broke out between union supporters competing for space, with both sides hurling rocks at each other, while television pictures showed at least one man firing a gun.
Others clutched sticks in the melee outside the entrance of Peron's former weekend retreat, where he was to be buried.
The burial was to cap a day of ceremonies infused with political symbolism ahead of next year's presidential elections. Decades after Peron's death, the Peronist party remains Argentina's biggest and most influential.
A former army colonel, Peron - who served as president three times - was first elected in 1946, a year after he was jailed for leading a military coup. Mass protests by his supporters helped him win freedom.
With his flamboyant wife Eva, popularly known as "Evita", at his side, Peron nationalised railroads and utilities and expanded worker benefits that made him a hero to working-class Argentines.
But he was also criticised as authoritarian, and amid economic turmoil, he was toppled in a military coup in 1955, three years after Evita died.
Argentine officials had been working for years to relocate Peron but faced legal obstacles, including a challenge from a woman who for more than a decade has been trying to prove she is his only child.
An agreement allowing forensic experts to extract samples from his body for possible DNA testing last week allowed the move to go forward.
After spending 18 years in exile in Spain, Peron returned to
Argentina in 1971 and was elected president two years later before dying in office. His third wife, Isabel, succeeded him before being overthrown by the military in 1976.
In 1987, robbers broke into the crypt and used an electric saw to slice off his hands in a case that has never been solved.