Goulart's remains were exhumed yesterday under police guard at a cemetery at Sao Borja, near the Argentinian border some 600 kilometres (400 miles) from the southern city of Porto Alegre, an AFP photographer reported.
Goulart, in office from 1961 to 1964, is suspected of having been poisoned under the Condor plan, a program of repression Latin American military regimes put in place to quash opposition in the 1970s and 1980s.
Given the local summer heat, the exhuming of the former leader took place just after dawn in the presence of Argentine and Uruguayan experts.
A Red Cross expert was also on hand as an observer.
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Goulart, nicknamed Jango, was ousted in a 1964 coup and officially died of a heart attack in Argentina in 1976, when Brazil's neighbour likewise saw a military regime seize power.
"This is an historic moment. Every democratic nation must preserve the truth," said Justice Minister Jose Eduardo Cardozo, who noted the known existence of documents suggesting Goulart may have been murdered.
"He was under surveillance and secret service agents entered his house. If they entered to steal a letter or documents they could poison some medicine or his food," a national truth commission investigating the military years recently told AFP.
Today, Goulart's remains will be taken to the capital Brasilia to receive full posthumous state honors.
Current Brazilian President Dilma Rousseff is expected to attend.