Bolsonaro has been arrested after authorities found he posed a definite escape threat while under domestic detention.
The former head of state was convicted of planning a government overthrow in September and sentenced more than over two decades in jail, but he was staying under house arrest pending appeals.
High Court Judge Alexandre de Moraes said the move to detain the septuagenarian politician was a safety action after "new facts" came to light.
This involved trying to remove his electronic bracelet and a summons to a public vigil that could enable a potential flight.
In a paperwork permitting the detention, the magistrate said intelligence from the centre monitoring Bolsonaro's house arrest suggested the ex-president's aim to disable the surveillance device to secure accomplishment in his getaway".
This, it said, would be "facilitated by the confusion caused by the gathering called by his son.
His offspring, Flávio Bolsonaro, who works as a senator, called for a gathering of his supporters near the former president's residence to take place on the weekend.
The senator wrote on online platforms on last Friday: "Are you going to fight for your country, or see it all from your mobile device there on your settee? I urge you to battle with us."
He said the gathering would be so followers could "pray for his health and for the reestablishment of democratic governance in our nation."
Part of the judge's decision was the potential of his move to foreign missions near the dwelling, considering that the investigations revealed a record of planning to seek refuge through a embassy office", a announcement said.
The legal document underscores that the American diplomatic mission in the capital, Brasilia, is positioned around 13km from Bolsonaro's home.
The former president's legal troubles have provoked anger from fellow populist conservative United States President President Trump, leading him to impose a 50% tariff on Brazilian product imports.
Bolsonaro is being detained in a national police facility in Brazil's capital city and will have a custody hearing on the next day.
It was only on the previous day that the former president's lawyers asked the Top Court to authorize him to fulfill his full incarceration period under house arrest, with tracking devices.
They also petitioned that Bolsonaro be authorized to depart his residence for medical care, saying he demanded frequent medical attention for respiratory ailments and other ailments.
Bolsonaro was convicted of orchestrating a scheme aimed at keeping him in power after he was defeated in the presidential race to his ideological adversary, President Lula.
Top judicial officials said that he was aware of a plan which encompassed plans to kill his opponent and his running partner, Geraldo Alckmin, and to detain and kill Justice Moraes - the High Court judge who has been managing his judicial proceedings.
The scheme was stopped because it didn't receive the endorsement of the military leaders. His successor was sworn in without issue on January 1st, 2023.
But a following week, on 8 January, many Bolsonaro supporters attacked and damaged public facilities in the national capital, BrasÃlia.
The law enforcement took action and around 1,500 people were detained.
The judges found that the protesters had been provoked by Bolsonaro whose plan, they said, was for the country's army to take action, bring back stability and return him to office.
At the moment, Bolsonaro's lawyers called the over 27-year sentence extremely harsh.
He was also banned from campaigning for office until 2060 - a decade minus two years after the completion of his term.
The former president called the legal proceedings a "witch hunt and said it was designed to prevent him running in the 2026 national vote.
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