Bolsonaro has been arrested after authorities found he posed a concrete flight risk while under home confinement.
The former head of state was sentenced of planning a armed takeover in last fall and handed more than 27 years in prison, but he remained under home detention pending court reviews.
Top Judicial Official Alexandre de Moraes said the action to imprison the 70-year-old politician was a preventative measure after recent developments came to light.
This involved trying to remove his ankle monitor and a call for a public vigil that could enable a potential flight.
In a paperwork permitting the custody, the judge said intelligence from the centre monitoring the former president's confinement suggested the former leader's "intention to break the tracking monitor to ensure success in his flight.
This, it said, would be assisted by the chaos caused by the protest called by his child.
His child, Flávio Bolsonaro, who works as a senator, called for a gathering of his backers near the former president's residence to take place on Saturday evening.
The senator wrote on online platforms on Friday: Do you plan to struggle for your country, or watch it all from your mobile device there on your couch? I invite you to battle with us."
He said the demonstration would be so backers could seek divine intervention for his health and for the reestablishment of democratic governance in our nation."
Part of the judge's decision was the chance of the former president's move to diplomatic missions near the dwelling, considering that the probes revealed a record of organizing to request asylum through a diplomatic representation", a statement said.
The judicial paperwork highlights that the United States embassy in the capital, the capital city, is positioned around 8 miles from his dwelling.
The former president's legal troubles have drawn the ire of fellow conservative nationalist US President Trump, prompting him to implement a fifty percent tax on imports of Brazilian goods.
The former president is being held in a national police facility in the capital and will experience a custody hearing on the following day.
It was only on last Friday that the ex-leader's attorneys asked the Supreme Court to permit him to complete his entire prison term under home confinement, with tracking devices.
They also petitioned that the former president be permitted to depart his residence for medical care, saying he needed frequent medical attention for respiratory ailments and other illnesses.
He was convicted of heading a scheme aimed at keeping him in power after he was defeated in the 2022 election to his left-wing rival, Luiz Inácio Lula da Silva.
High Court judges said that he had knowledge of a scheme which included plans to assassinate Lula and his VP candidate, Alckmin, and to detain and kill the presiding judge - the High Court judge who has been presiding over his judicial proceedings.
The scheme was prevented because it couldn't obtain the backing of the military leaders. His successor was took office without incident on 1 January 2023.
But a seven days after, on 8 January, many his backers stormed and vandalised government buildings in the federal district, Brazil's capital.
The police stepped in and around approximately 1,500 persons were taken into custody.
The judges found that the protesters had been incited by Bolsonaro whose plan, they said, was for the Brazilian military to step in, restore order and reinstate his authority.
At the moment, the legal team called the over 27-year sentence unreasonably severe".
He was also prohibited from campaigning for office until twenty-sixty - eight years later after the end of his sentence.
The former president called the court case a political persecution and said it was designed to prevent him participating in the 2026 presidential election.
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