"The president is in good health at the moment and is in his residence," his office said in a statement.
Since the beginning of the virus outbreak, Bolsonaro has minimised the risks of what he initially called "a little flu" and flouted social distancing rules and containment measures, such as wearing a mask in public.
Brazil is the second worst-hit country in the world by the pandemic, with more than 65,000 deaths and at least 1.6 million cases.
Bolsonaro had been tested three times previously -- all came back negative.
On Monday, the far-right leader made more changes to weaken a law that would require citizens to wear face masks in public.
He had already watered down the bill Friday by vetoing several articles, such as requiring employers to supply face masks for their staff and another mandating that public authorities should provide face coverings for "economically vulnerable people."