Bolsonaro has been taken into custody after authorities determined he posed a definite escape threat while under domestic detention.
The one-time leader was convicted of plotting a military coup in September and handed more than over two decades in jail, but he continued under home detention pending appeals.
High Court Judge Justice Moraes said the action to imprison the 70-year-old politician was a preventative measure after "new facts" were revealed.
This encompassed trying to remove his electronic bracelet and a summons to a public vigil that could enable a chance to flee".
In a filing authorising the custody, the magistrate said intelligence from the unit overseeing his home detention suggested the former leader's "intention to break the tracking monitor to guarantee victory in his escape.
This, it said, would be assisted by the disorder caused by the gathering called by his son.
His child, his son Flávio, who works as a senator, called for a meeting of his supporters near Bolsonaro's home to take place on Saturday evening.
His son wrote on online platforms on last Friday: Will you battle for your nation, or watch it all from your phone there on your settee? I call on you to battle with us."
He said the gathering would be so supporters could "pray for his well-being and for the reestablishment of democratic governance in our country."
Part of the magistrate's ruling was the chance of his move to diplomatic missions near the residence, considering that the investigations revealed a history of arranging to ask for protection through a embassy office", a statement said.
The court filing underscores that the American diplomatic mission in the capital, the capital city, is located around 8 miles from the former president's residence.
The former president's legal troubles have generated frustration from fellow conservative nationalist American leader Trump, prompting him to implement a fifty percent tax on goods coming from Brazil.
Bolsonaro is being held in a Federal Police station in Brasilia and will experience a detention review on the following day.
It was only on last Friday that the his legal team asked the Supreme Court to permit him to fulfill his full incarceration period under house arrest, with tracking devices.
They also requested that he be allowed to leave his home for medical care, saying he demanded frequent medical attention for lung conditions and other health problems.
Bolsonaro was found guilty of leading a scheme aimed at maintaining his control after he failed to win the presidential race to his political opponent, Lula.
High Court judges said that he knew of a plan which encompassed plans to assassinate the current president and his running partner, his vice-presidential candidate, and to arrest and execute Alexandre de Moraes - the High Court judge who has been managing the former president's case.
The scheme was thwarted because it didn't receive the backing of the armed forces officials. The current president was took office without incident on 1 January 2023.
But a week later, on the eighth of January, many Bolsonaro supporters stormed and vandalised public facilities in the federal district, the capital city.
The law enforcement stepped in and around 1,500 people were arrested.
The judges found that the protesters had been provoked by Bolsonaro whose scheme, they said, was for the Brazilian military to intervene, restore order and return him to office.
At the period, Bolsonaro's lawyers called the over 27-year sentence "absurdly excessive.
He was also prohibited from campaigning for office until the year 2060 - eight years after the completion of his term.
The one-time head of state called the court case a political persecution and said it was intended to stop him running in the 2026 presidential election.
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