The new defense minister, General Walter Braga Netto, presented Army General Paulo Sergio Nogueira de Oliveira, Navy Admiral Almir Garnier and Air Force commander Brigadier Carlos Almeida Baptista Jr at a brief ceremony.
Braga Netto said the trio would all be "faithful to their constitutional missions of defending the homeland, guaranteeing constitutional powers and guaranteeing democratic freedoms."
Bolsonaro has overhauled his government in the face of mounting criticism for an explosion of Covid-19 deaths, replacing his foreign, defense and justice ministers, along with his chief of staff, the attorney general and the military's top brass.
Last week, he also installed his fourth health minister of the pandemic.
Bolsonaro, who comes up for re-election in October 2022, faces sliding popularity and growing pressure over his handling of the pandemic, including from key allies in Congress and the business world.
On Wednesday, the country ended its deadliest month of the coronavirus crisis with more than 66,570 deaths -- more than double the previous record.
The new military commanders are replacing Army General Edson Pujol, Navy Admiral Ilques Barbosa and Air Force Lieutenant-Brigadier Antonio Carlos Bermudes.
No reason was given for their departure, but analysts say the three chiefs were dismayed by Bolsonaro's surprise dismissal of former defense minister Fernando Azevedo.
Azevedo himself resigned because he was "uncomfortable with Bolsonaro's use of the military for political ends," journalist Merval Pereira wrote in newspaper Globo.
Bolsonaro, a former army captain, frequently boasts of having the military's backing, and has packed his government with officers.
He is openly nostalgic for Brazil's 1964-1985 military dictatorship, despite its rights violations, including the kidnapping and torture of dissidents.
The armed forces have since carefully rebuilt an apolitical image of national service.
But Bolsonaro's hardline base has put that to the test with calls to reinstall military rule with him at the top -- talk the president is accused of fanning.
Braga Netto said Tuesday the military dictatorship which took power on March 31, 1964, was something to be "celebrated."
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