Bolsonaro has been detained after authorities found he posed a definite escape threat while under domestic detention.
The former head of state was sentenced of plotting a military coup in September and handed more than 27 years in incarceration, but he was staying under home detention pending appeals.
High Court Judge Justice Moraes said the move to detain the 70-year-old politician was a precautionary step after fresh information came to light.
This included seeking to disable his tracking device and a invitation to a supporters' gathering that could "allow for a potential flight.
In a document approving the custody, Justice Moraes said data from the centre monitoring Bolsonaro's house arrest suggested the one-time head of state's aim to disable the tracking monitor to ensure success in his escape.
This, it said, would be assisted by the disorder caused by the demonstration called by his offspring.
His son, Flávio, who works as a congressional representative, called for a meeting of his followers near Bolsonaro's home to take place on Saturday night.
Flávio Bolsonaro wrote on online platforms on the previous day: Do you plan to struggle for your nation, or observe everything from your mobile device there on your sofa? I invite you to battle with us."
He said the vigil would be so supporters could seek divine intervention for his well-being and for the reestablishment of democratic governance in our nation."
Part of Justice Moraes's decision was the possibility of his move to diplomatic missions near the residence, considering that the inquiries revealed a history of organizing to seek refuge through a embassy office", a declaration said.
The court filing highlights that the US embassy in the federal district, Brasilia, is positioned around 13km from Bolsonaro's home.
His judicial problems have provoked anger from fellow right-wing populist American leader Trump, leading him to enact a half-rate duty on imports of Brazilian goods.
Bolsonaro is being detained in a federal law enforcement building in Brasilia and will have a detention review on the following day.
It was only on the previous day that the his legal team asked the High Court to authorize him to fulfill his full incarceration period under home confinement, with electronic monitoring.
They also asked that the former president be allowed to depart his residence for healthcare, saying he required frequent medical attention for pulmonary infections and other ailments.
The former president was determined responsible of orchestrating a plot aimed at retaining his authority after he lost the national vote to his ideological adversary, Lula.
Supreme Court justices 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 arrest and execute the presiding judge - the High Court judge who has been presiding over Bolsonaro's trial.
The scheme was thwarted because it couldn't obtain the support of the armed forces officials. His successor was inaugurated without incident on January 1st, 2023.
But a week later, on the eighth of January, numerous Bolsonaro supporters attacked and damaged public facilities in the capital, Brazil's capital.
The security forces took action and around approximately 1,500 persons were taken into custody.
The justices found that the rioters had been encouraged by the former president whose strategy, they said, was for the Brazilian military to step in, reestablish control and bring him back to power.
At the period, his attorneys called the decades-long sentence "absurdly excessive.
He was also prohibited from campaigning for office until 2060 - a decade minus two years after the end of his sentence.
The one-time head of state called the trial a political persecution and said it was designed to prevent him participating in the next presidential race.
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