The announcement came five days after President Jair Bolsonaro said he was over his illness and had resumed his normal work routine.
Michelle Bolsonaro, 38, "is in good health and will follow all established protocols," the president's office said.
Bolsonaro, 65, has faced criticism for his handling of the pandemic as Brazil has surged to become the country with the second-highest number of infections and deaths in the world.
Brazil's first lady Michelle Bolsonaro tested positive for the new coronavirus Thursday, the government said, after her husband spent two weeks in quarantine with it.
The announcement came five days after President Jair Bolsonaro said he was over his illness and had resumed his normal work routine.