A judge in Argentina, where Fangio was born and died, ordered the exhumation so DNA samples can be used to try and resolve two paternity cases brought about by men in their seventies.
Fangio, who won the F1 World Championship five times in the 1950s, never married and did not admit to having any children.
However, his biographers have claimed he had a relationship with a woman called Andrea Berruet for two decades.
Ms Berruet’s son, Oscar Espinosa, a former Formula 3 driver known by colleagues as “Cancho” Fangio, is one of the men who has filed a paternity lawsuit.
The other man claiming to be Fangio’s son is Ruben Vazquez.
Mr Vazquez has claimed he is not interested in inheriting any of his alleged father’s fortune, adding: “I just want to be recognised for the Fangio surname.”
Juan Manuel Fangio left a large part of his estate to the Juan Manuel Fangio Museum in Buenos Aires, which houses a collection of cars, trophies, photographs and other memorabilia.
Many people consider Fangio to be the greatest racing driver of all time and his record of five World Championships stood for 45 years until German Michael Schumacher won his sixth title in 2003.
Schumacher, now 46, had huge respect for Fangio and paid tribute to him after he died.
In an interview just before what would have been the late legend’s 100th birthday, Schumacher, who met his hero in 1992, said: “The drivers in Fangio’s time were all very courageous; it makes you realise how fortunate we are today with the build of our cars and the high safety standards.”
Schumacher, who marked his 20th wedding anniversary with wife Corinna this week, is still on the long road to recovery after a skiing accident in the French Alps put him in a coma for six months in December 2013.
Schumacher spent months in a hospital in France before being moved to recover in his family home, which he has been recuperating in for nearly a year.
Mrs Schumacher, their children Gina Marie, 16, and Mick, 14, have kept details of the former Ferrari driver’s recovery private but Mick did reveal last year that his father was getting better “very slowly”.
Fangio was born in Buenos Aires, Argentina on June 24 1911 and died in the same city on July 17 1995, aged 84.
He won the Formula One World Drivers’ Championship with four different teams – Alfa Romeo, Maserati, Mercedes and Ferrari – a feat no other driver has achieved.
His nephew Juan Manuel Fangio II, now aged 58, was also a successful racing driver.
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