But his companion, Cecilia Matos, said he had vowed never to return as long as Hugo Chavez remained president.
She later relented, saying she would not oppose a burial in Venezuela.
Blanca Rodriguez de Perez had obtained a court order to stop him being buried in Miami until the dispute was solved.
His body has been in a mortuary and temporary mausoleum since his death last December at the age of 88.
The casket containing his remains, draped in a Venezuela flag, has now been taken from the mausoleum and carried away in a hearse, in preparation for a flight home.
His body is expected to arrive in Venezuela later on Tuesday, accompanied by a convoy of cars from the airport to the capital, Caracas.
His body will lie in state at the headquarters of his Democracy Action party to allow people to pay their respects, before a public funeral on Thursday at a Caracas cemetery.
Corruption conviction Perez was twice Venezuela's president, from 1974 to 1979 and again between 1989 and 1993.
His first term was marked by a transformation of Venezuela's economy because of a sudden increase in oil revenues.
But the second was marred by allegations of corruption.
Forced to leave office in 1993, he was then sentenced to 28 months in prison for the misappropriation of millions of dollars in public funds.
He spent the first few months in a jail in Caracas, but was then allowed to serve the rest of his term under house arrest. Perez always denied any wrongdoing.
He had survived two coup attempts in 1992, the first of which was led by Mr Chavez, who was then a young army lieutenant-colonel.
Based in Miami, Perez fought attempts to extradite him to stand trial for his role in putting down riots in 1989.
He was accused of sending troops into the streets to fire indiscriminately on protesters during the so-called Caracazo riots.