Bolsonaro has been taken into custody after authorities concluded he posed a definite escape threat while under home confinement.
The former head of state was sentenced of plotting a armed takeover in the ninth month and sentenced more than 27 years in incarceration, but he remained under house arrest pending legal challenges.
High Court Judge the presiding justice said the move to detain the 70-year-old politician was a precautionary step after "new facts" were revealed.
This encompassed seeking to disable his electronic bracelet and a invitation to a demonstration that could "allow for a chance to flee".
In a document approving the custody, Justice Moraes said information from the centre monitoring the former president's confinement suggested the ex-president's "intention to break the tracking monitor to secure accomplishment in his flight.
This, it said, would be assisted by the disorder caused by the demonstration called by his offspring.
His child, Flávio, who works as a senator, called for a meeting of his followers near Bolsonaro's home to take place on Saturday evening.
The senator wrote on online platforms on the previous day: Do you plan to struggle for your nation, or watch it all from your phone there on your couch? I call on you to fight with us."
He said the gathering would be so followers could seek divine intervention for his well-being and for the reestablishment of democratic governance in our land."
Part of the judge's determination was the potential of his transfer to diplomatic missions near the residence, considering that the investigations revealed a record of organizing to request asylum through a embassy office", a statement said.
The legal document highlights that the US embassy in the national capital, Brasilia, is situated around 8 miles from his dwelling.
Bolsonaro's legal woes have provoked anger from fellow conservative nationalist United States President Trump, leading him to impose a 50% tariff on goods coming from Brazil.
The former president is being detained in a federal law enforcement building in the capital and will have a imprisonment assessment on Sunday.
It was only on the previous day that the ex-leader's attorneys asked the High Court to allow him to complete his entire prison term under house arrest, with digital surveillance.
They also petitioned that he be allowed to exit his dwelling for medical care, saying he demanded frequent medical attention for respiratory ailments and other ailments.
Bolsonaro was found guilty of orchestrating a scheme aimed at retaining his authority after he failed to win the 2022 election to his left-wing rival, President Lula.
Supreme Court justices said that he was aware of a plot which included plans to assassinate Lula and his VP candidate, his vice-presidential candidate, and to detain and kill Alexandre de Moraes - the High Court judge who has been managing the former president's case.
The conspiracy was stopped because it failed to get the backing of the army and air force commanders. His successor was inaugurated without incident on January 1st, 2023.
But a week later, on 8 January, many his backers invaded and destroyed official structures in the national capital, BrasÃlia.
The law enforcement stepped in and around 1,500 people were arrested.
The magistrates found that the rioters had been provoked by the former president whose plan, they said, was for the country's army to step in, restore order and return him to office.
At the time, his attorneys called the over 27-year sentence unreasonably severe".
He was also barred from seeking elected position until twenty-sixty - eight years later after the completion of his term.
The ex-leader called the court case a "witch hunt and said it was designed to prevent him running in the 2026 national vote.
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