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 found guilty of planning a military coup in the ninth month and given more than a 27-year term in prison, but he continued under confinement pending appeals.
High Court Judge Alexandre de Moraes said the move to detain the elderly politician was a preventative measure after recent developments emerged.
This included seeking to disable his ankle monitor and a invitation to a public vigil that could facilitate a possible escape.
In a paperwork permitting the arrest, the magistrate said information from the facility tracking his home detention suggested the one-time head of state's plan to remove the electronic ankle bracelet to guarantee victory in his flight.
This, it said, would be assisted by the chaos caused by the protest called by his offspring.
His son, Flávio, who holds office as a congressional representative, called for a assembly of his followers near his father's house to take place on Saturday evening.
The senator wrote on digital networks on Friday: Will you battle for your nation, or see it all from your mobile device there on your settee? I call on you to battle with us."
He said the demonstration would be so supporters could seek divine intervention for his well-being and for the restoration of democratic rule in our land."
Part of Justice Moraes's decision was the possibility of the former president's "relocation to diplomatic missions near the home, considering that the probes revealed a background of arranging to ask for protection through a embassy office", a statement said.
The legal document highlights that the United States embassy in the national capital, Brasilia, is located around 13km from Bolsonaro's home.
The former president's legal troubles have drawn the ire of fellow conservative nationalist US President Donald Trump, causing him to enact a fifty percent tax on imports of Brazilian goods.
He is being detained in a federal law enforcement building in Brasilia and will undergo a custody hearing on the following day.
It was only on last Friday that the ex-leader's attorneys asked the Supreme Court to authorize him to fulfill his full incarceration period under domestic detention, with digital surveillance.
They also requested that Bolsonaro be permitted to depart his residence for medical treatment, saying he demanded ongoing care for respiratory ailments and other health problems.
He was found guilty of leading a plot aimed at maintaining his control after he failed to win the 2022 election to his political opponent, Lula.
High Court judges said that he had knowledge of a scheme which encompassed plans to murder the current president and his vice-presidential running mate, his vice-presidential candidate, and to imprison and murder the presiding judge - the High Court judge who has been overseeing the former president's case.
The conspiracy was prevented because it couldn't obtain the backing of the army and air force commanders. The current president was inaugurated without incident on January 1st, 2023.
But a seven days after, on the eighth of January, numerous his followers stormed and vandalised official structures in the federal district, the capital city.
The law enforcement intervened and around 1,500 people were taken into custody.
The justices found that the demonstrators had been encouraged by him whose strategy, they said, was for the national armed forces to step in, reestablish control and return him to office.
At the period, his attorneys called the 27 years and three months sentence "absurdly excessive.
He was also prohibited from running for public office until the year 2060 - a decade minus two years after the completion of his term.
The former president called the court case a "witch hunt and said it was aimed at blocking him competing in the 2026 national vote.
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