Bolsonaro has been arrested after authorities concluded he posed a serious risk of fleeing while under home confinement.
The ex-president was convicted of planning a military coup in September and sentenced more than 27 years in incarceration, but he continued under home detention pending appeals.
Top Judicial Official Justice Moraes said the action to imprison the 70-year-old politician was a safety action after recent developments emerged.
This encompassed trying to remove his tracking device and a invitation to a public vigil that could facilitate a potential flight.
In a document approving the arrest, Justice Moraes said intelligence from the unit overseeing Bolsonaro's house arrest suggested the ex-president's "intention to break the electronic ankle bracelet to guarantee victory in his escape.
This, it said, would be made easier by the confusion caused by the demonstration called by his child.
His offspring, his son Flávio, who serves as a legislator, called for a assembly of his supporters near his father's house to take place on Saturday night.
Flávio Bolsonaro wrote on social media on the previous day: Do you plan to struggle for your homeland, or observe everything from your smartphone there on your sofa? I call on you to fight with us."
He said the gathering would be so supporters could seek divine intervention for his well-being and for the return of democracy in our country."
Part of the judge's determination was the chance of Bolsonaro's "relocation to diplomatic missions near the residence, considering that the investigations revealed a record of arranging to request asylum through a diplomatic representation", a statement said.
The court filing emphasizes that the United States embassy in the federal district, Brazil's capital, is located around 13km from his dwelling.
The former president's legal troubles have provoked anger from fellow right-wing populist American leader Donald Trump, prompting him to impose a 50% tariff on Brazilian product imports.
The former president is being detained in a national police facility in Brasilia and will undergo 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 serve his whole jail sentence under house arrest, with electronic monitoring.
They also asked that he be authorized to leave his home for medical care, saying he required frequent medical attention for lung conditions and other health problems.
He was found guilty of leading a scheme aimed at retaining his authority after he failed to win the national vote to his political opponent, Luiz Inácio Lula da Silva.
Supreme Court justices said that he knew of a scheme which involved plans to kill the current president and his running partner, his vice-presidential candidate, and to detain and kill Alexandre de Moraes - the High Court judge who has been managing his judicial proceedings.
The conspiracy was thwarted because it didn't receive the endorsement of the army and air force commanders. The current president was sworn in without issue on 1 January 2023.
But a week later, on January 8th, many Bolsonaro supporters stormed and vandalised government buildings in the federal district, Brazil's capital.
The police intervened and around fifteen hundred individuals were detained.
The judges found that the rioters had been incited by the former president whose plan, they said, was for the country's army to take action, reestablish control and return him to office.
At the period, Bolsonaro's lawyers called the 27 years and three months sentence extremely harsh.
He was also banned from seeking elected position until the year 2060 - eight years later after the completion of his term.
The former president called the court case a political persecution and said it was intended to stop him participating in the 2026 presidential election.
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