A loyal ally of President Jair Bolsonaro, Araujo represents an ideological wing of the right-wing populist administration whose attacks against China, environmentalists and the left were increasingly seen as noisy distractions from tackling Brazil's raging pandemic.
"For the first time in history, the commanders of all three branches of the armed forces presented their joint resignation in disagreement with the president", said newspaper Folha de Sao Paulo.
Mr Melo said the military itself had so far refrained from politics, but added: "Will this resistance continue?"
Bolsonaro is a retired army captain, and he has packed his government with military officials.
"The latest changes have a twin objective: first, because (Bolsonaro) needs to free up cabinet posts for his new centrist allies, and second, because he is preparing for a possible political crisis and wants to surround himself with extremely loyal people, especially in the armed forces", political analyst Oliver Stuenkel said.
He has also criticised the Supreme Court for upholding local governments' rights to adopt pandemic restrictions that he adamantly opposes, arguing that the economic effects are worse than the disease itself. "The change at the Ministry of Defense was completely unexpected, and created a lot of confusion".
Earlier this month, Bolsonaro began mentioning the armed forces in connection with his dispute with state governors and mayors over restrictive measures meant to slow the spread of the coronavirus in Latin America's largest nation.
"My army doesn't go to the street to force people to stay at home", Bolsonaro told reporters on March 19. There are fresh concerns he could deploy soldiers to override such restrictions.
"He wants people who will do whatever he wants, and so it is extremely risky", Traumann said.
Vice President Hamilton Mourao, an army general, said there was "zero" risk of an anti-democratic intervention by the military against Congress or the courts.
Bolsonaro saw his popularity rise previous year, thanks to a generous pandemic welfare aid program. Early polls indicate he would be a formidable challenger in next year's election.
His strong affinity with former US President Donald Trump is believed to have made him unpopular with the Joe Biden White House.
The departure of Brazil's three top military commanders comes a day after Bolsonaro's most dramatic cabinet overhaul since taking power, included the shock departure of his defence minister.
Mr Bolsonaro on Monday carried out a shake-up of top Cabinet positions that was initially seen as a response to demands for a course correction by politicians, diplomats and economists, particularly over his handling of the pandemic that has caused more than 300,000 deaths in Brazil.
Bolsonaro also tapped a retired army general to take over state-run oil behemoth Petrobras, seeking to appeal to supportive truck drivers who had threatened to strike over fuel price increases.
Chinese-developed CoronaVac is now the most-administered Covid-19 vaccine in Brazil, but only because the government of Sao Paulo state defied resistance from the Bolsonaro administration to acquire it.
With an average of some 2,400 deaths each day, Brazil accounts for a quarter of daily COVID-19 fatalities worldwide, according to Johns Hopkins University data.