Bolsonaro has been taken into custody after authorities determined he posed a definite escape threat while under home confinement.
The former head of state was sentenced of orchestrating a armed takeover in September and handed more than over two decades in jail, but he was staying under house arrest pending court reviews.
High Court Judge Alexandre de Moraes said the move to detain the elderly politician was a precautionary step after "new facts" emerged.
This involved trying to remove his ankle monitor and a invitation to a public vigil that could "allow for a chance to flee".
In a filing authorising the arrest, the judge said intelligence from the centre monitoring the former president's confinement suggested the ex-president's plan to remove the electronic ankle bracelet to secure accomplishment in his flight.
This, it said, would be made easier by the disorder caused by the demonstration called by his child.
His child, Flávio Bolsonaro, who works as a senator, called for a assembly of his supporters near the former president's residence to take place on Saturday evening.
His son wrote on social media on the previous day: "Are you going to fight for your nation, or observe everything from your phone there on your settee? I invite you to battle with us."
He said the demonstration would be so backers could offer prayers for his health and for the reestablishment of democratic governance in our nation."
Part of Justice Moraes's decision was the possibility of Bolsonaro's transfer to embassies near the dwelling, considering that the inquiries revealed a history of planning to ask for protection through a embassy office", a announcement said.
The judicial paperwork highlights that the US embassy in the capital, Brazil's capital, is positioned around 8 miles from the former president's residence.
His judicial problems have generated frustration from fellow right-wing populist US President Trump, prompting him to impose a fifty percent tax on Brazilian product imports.
He is being held in a national police facility in Brazil's capital city and will have a imprisonment assessment on the following day.
It was only on Friday that the his legal team asked the Supreme Court to authorize him to fulfill his full incarceration period under house arrest, with digital surveillance.
They also asked that Bolsonaro be permitted to depart his residence for medical care, saying he needed frequent medical attention for respiratory ailments and other health problems.
The former president was found guilty of heading a plot aimed at keeping him in power after he failed to win the 2022 election to his ideological adversary, President Lula.
Top judicial officials said that he knew of a plan which encompassed plans to murder the current president and his running partner, his vice-presidential candidate, and to detain and kill Alexandre de Moraes - the top judicial official who has been overseeing the former president's case.
The scheme was stopped because it couldn't obtain the endorsement of the armed forces officials. The current president was inaugurated without problem on 1 January 2023.
But a seven days after, on the eighth of January, many his backers stormed and vandalised government buildings in the federal district, Brasília.
The security forces stepped in and around approximately 1,500 persons were arrested.
The magistrates found that the rioters had been incited by Bolsonaro whose plan, they said, was for the country's army to step in, reestablish control and return him to office.
At the moment, Bolsonaro's lawyers called the over 27-year sentence "absurdly excessive.
He was also barred from campaigning for office until the year 2060 - eight years later after the conclusion of his imprisonment.
The ex-leader called the trial a political persecution and said it was designed to prevent him competing in the 2026 presidential election.
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