Brazil has suffered the second largest COVID-19 outbreak, just after the United States.
However, the president has often been seen defying restrictions such as mask wearing and social distancing.
There have been explosions of infections across the world, including Iran, which announced 200 new deaths on Tuesday. He took over after his predecessor, a doctor and health care consultant, quit in protest over Bolsonaro's support for hydroxychloroquine. He hasn't said whether he took any additional tests for the disease since.
When the number of deaths in Brazil climbed past 5,000, Bolsonaro, whose middle name means messiah, said: "So what?"
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Experts are still struggling to understand COVID-19, and the World Health Organization said it was open to new research after scientists lobbied for it to stress that the virus can spread through the air farther and for longer than initially believed. That is why he submitted for a test, and announced on Tuesday that it came back positive. "It's going to get you".
Mr Bolsonaro, who has played down the severity of the disease, which he has called a "little flu", received his latest test after reportedly developing symptoms associated with COVID-19, including a fever, on Sunday.
Bolsonaro has previously appeared in public and at rallies without a mask, even hugging supporters. "The president, at this time, is in good health and remains at his residence", his office said on Monday.
He said he cancelled a trip this week to Brazil's northeast region and will continue working via videoconference and receive rare visitors when he needs to sign a document.
Bolsonaro has repeatedly visited the hospital since taking office, requiring several operations to fix his intestines after he was stabbed on the campaign trail in 2018.
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Over the weekend, the Brazilian leader celebrated the US Independence Day with the nation's ambassador to Brazil, then shared pictures on social media showing him in close quarters with the ambassador, several ministers and aides.
"The message is that this virus is unpredictable and does not respect race, class or people in power, despite security around any president", Espinal said.
This is the fourth coronavirus test he has taken - the first three had come back negative.
Bolsonaro's diagnosis comes just three days after he had lunch at the home of the USA ambassador to Brazil, Todd Chapman, in the capital, Brasília.
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