"We remove content on Facebook and Instagram that violates our terms of use, which do not allow misinformation that could cause physical harm to individuals," Facebook said in a statement in Portuguese.
Twitter on Sunday explained it had removed the videos in accordance with its recently expanded global rules on managing content that contradicted public health information from official sources, and could put people at greater risk of transmitting COVID-19.
The videos showed the far-right leader flouting his government's social distancing guidelines by mixing with supporters on the streets of Brasilia on Sunday and urging them to keep the economy going.
On Saturday, Health Minister Luiz Henrique Mandetta highlighted the importance of containment as a means of fighting the coronavirus. Brazil has reported the most coronavirus cases in Latin America so far: 4,256, with 136 deaths.
On Monday, Mandetta again stressed the importance of social distancing in order to slow the virus.
"At this time, we must maintain the highest degree of social distancing, so that we can... give time for the (health) system to strengthen itself," he said.
Bolsonaro has repeatedly downplayed the seriousness of the coronavirus, describing it as "a flu" and calling for schools and shops to re-open, with self-isolation necessary only for people over the age of 60.
On Monday, his leading opponents urged him to resign in a joint letter, arguing that he committed a crime with his mishandling of the coronavirus pandemic.
"Bolsonaro is more than just a political problem, he has become a public-health problem. He should resign," said the statement, which was signed by a dozen leading left-wing figures.