The 65-year-old leader, who has previously dismissed the virus, will resume his travel schedule after isolating for weeks inside Alvorada Palace - an experience he has described as "just horrible".
He said on July 7 he had been diagnosed with the disease - which has killed more than 87,000 Brazilians - before confirming he was Covid-free on Saturday.
It comes just three days after he tested positive on Wednesday.
Mr Bolsonaro posted a photo of himself with a box of the anti-malaria drug hydroxychloroquine, although this has not been proven to be an effective treatment for the virus.
The president - who has been a leading skeptic in relation to the disease - often mingled with crowds prior to his diagnosis.
He had spent many weekends since the beginning of the pandemic in close proximity to supporters, sometimes without wearing a mask.
On Thursday, he was photographed without a mask while talking to some sweepers in the garden of the presidential residence.
Shortly after announcing the negative result, the president Mr Bolsonaro greeted supporters outside a bike shop, after going for a spin around Brasilia.
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