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He was found by his son in his private apartments at 0830 local time.
Dr Vargas, who shot himself through the heart, left a dramatic suicide note that was broadcast on national radio just two hours after his body was discovered.
In it he complained his efforts to "liberate" the people of Brazil had been hampered by foreign interests which he blamed for the economic crisis that is gripping the nation.
His letter read: "Nothing remains except my blood. I gave you my life, now I give you my death. I choose this way to defend you, for my soul will be with you, my name shall be a flag for your struggle."
It ended: "I take the first step to eternity. I leave life to enter history."
The president's death comes at a time of serious unrest in the country.
Inflation is at an all-time high and wage increases are not keeping pace with prices.
Discontent with Dr Vargas came to ahead after the attempted assassination of opposition newspaper editor and Congress candidate Carlos Lacerda earlier this month.
Mr Lacerda, a fierce critic of the Vargas regime, was wounded in the foot during the attack on 5 August and an air force officer was killed, sparking fury among the Brazilian military.
The driver of the getaway car was later arrested and confessed that one of the killers was the president's bodyguard.
President Vargas seized power in the 1930 revolution, dissolved parliament seven years later and banned all political parties and trade unions. He censored the press and suppressed all opposition.
After the end of World War II in 1945 the president yielded to popular demand for greater democracy and was forced to step down by the army.
President Dutra was duly elected but in October 1950 Dr Vargas, now leader of the Brazilian Labour Party, was voted back into the presidency.
Three years on, Brazil's once thriving economy is riddled with foreign debt to the tune of $1,000 million, wages increases cannot keep up with price rises and there has been speculation that the Vargas regime is involved in corruption and dubious business deals.
In spite of widespread dissatisfaction with President Vargas, his death and suicide note sparked a wave of emotion.
Thousands attended his funeral at his birthplace in Sao Borja and there were riots in the then capital, Rio de Janeiro that were soon quelled by the armed forces.
Vice-president João Café Filho took over as head of state. Elections took place in 1955 and Juscelino Kubitschek was proclaimed president in 1956. He helped Brazil achieve rapid economic growth and moved the capital to Brasilia as part of moves to develop the interior.
Brazil's economy has a history of boom and bust, with its attempts at development hampered in the past by high inflation and one of the world's biggest foreign debts.
It has had to be bailed out in times of crisis, but economic reforms in the 1990s brought some stability to the country's finances. Reforms included privatisation and the opening up of its markets.
The government is under pressure to redress what some say is one of the world's most unfair distributions of wealth.
Much of the country's arable land is controlled by a handful of wealthy families, and the Movement of Landless Rural Workers (MST) is demanding land redistribution.
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