Bolsonaro has been detained after authorities concluded he posed a serious risk of fleeing while under house arrest.
The former head of state was sentenced of planning a government overthrow in September and given more than a 27-year term in prison, but he was staying under house arrest pending court reviews.
High Court Judge Justice Moraes said the action to imprison the 70-year-old politician was a safety action after recent developments came to light.
This involved trying to remove his tracking device and a call for a supporters' gathering that could enable a possible escape.
In a filing authorising the arrest, the magistrate said information from the unit overseeing the former president's confinement suggested the ex-president's "intention to break the tracking monitor to guarantee victory in his getaway".
This, it said, would be made easier by the chaos caused by the gathering called by his son.
His offspring, Flávio, who works as a congressional representative, called for a meeting of his supporters near Bolsonaro's home to take place on Saturday night.
Flávio Bolsonaro wrote on online platforms on Friday: Will you battle for your nation, or observe everything from your mobile device there on your settee? I invite you to battle with us."
He said the gathering would be so supporters could offer prayers for his physical condition and for the reestablishment of democratic governance in our nation."
Part of the judge's determination was the potential of Bolsonaro's transfer to foreign missions near the dwelling, considering that the inquiries revealed a background of organizing to request asylum through a embassy office", a declaration said.
The legal document highlights that the American diplomatic mission in the federal district, Brazil's capital, is positioned around 13km from the former president's residence.
His judicial problems have generated frustration from fellow right-wing populist US President President Trump, prompting him to enact a half-rate duty on imports of Brazilian goods.
Bolsonaro is being kept in a national police facility in Brazil's capital city and will have a detention review on the next day.
It was only on the previous day that the former president's lawyers asked the Top Court to allow him to fulfill his full incarceration period under house arrest, with tracking devices.
They also petitioned that he be permitted to exit his dwelling for medical care, saying he needed regular treatment for lung conditions and other health problems.
The former president was convicted of orchestrating a scheme aimed at retaining his authority after he lost the national vote to his ideological adversary, Lula.
Top judicial officials said that he had knowledge of a plan which included plans to kill his opponent and his VP candidate, Alckmin, and to detain and kill Justice Moraes - the Supreme Court justice who has been managing his judicial proceedings.
The conspiracy was prevented because it didn't receive the backing of the armed forces officials. His successor was inaugurated without incident on the first day of 2023.
But a week later, on 8 January, numerous his backers attacked and damaged government buildings in the federal district, Brasília.
The police took action and around approximately 1,500 persons were arrested.
The judges found that the rioters had been incited by him whose plan, they said, was for the Brazilian military to step in, bring back stability and reinstate his authority.
At the period, Bolsonaro's lawyers called the over 27-year sentence "absurdly excessive.
He was also banned from seeking elected position until twenty-sixty - eight years after the completion of his term.
The former president called the legal proceedings a "witch hunt and said it was designed to prevent him running in the 2026 national vote.
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