Bolsonaro has been taken into custody after authorities determined he posed a serious risk of fleeing while under domestic detention.
The former head of state was found guilty of plotting a military coup in the ninth month and handed more than over two decades in prison, but he was staying under house arrest pending appeals.
High Court Judge the presiding justice said the action to imprison the septuagenarian politician was a preventative measure after "new facts" were revealed.
This involved seeking to disable his ankle monitor and a call for a demonstration that could "allow for a possible escape.
In a paperwork permitting the detention, the judge said information from the facility tracking the former president's confinement suggested the former leader's aim to disable the surveillance device to secure accomplishment in his flight.
This, it said, would be assisted by the chaos caused by the protest called by his son.
His child, Flávio Bolsonaro, who serves as a legislator, called for a meeting of his backers near his father's house to take place on the weekend.
The senator wrote on digital networks on Friday: Do you plan to struggle for your nation, or see it all from your smartphone there on your sofa? I urge you to struggle with us."
He said the demonstration would be so backers could "pray for his well-being and for the restoration of democratic rule in our country."
Part of the judge's determination was the potential of his move to embassies near the dwelling, considering that the probes revealed a history of organizing to ask for protection through a embassy office", a declaration said.
The court filing underscores that the American diplomatic mission in the national capital, the capital city, is positioned around 8 miles from his dwelling.
His judicial problems have generated frustration from fellow populist conservative United States President Trump, causing him to enact a 50% tariff on goods coming from Brazil.
Bolsonaro is being detained in a Federal Police station in Brasilia and will undergo a custody hearing on the next day.
It was only on Friday that the ex-leader's attorneys asked the Top Court to permit him to serve his whole jail sentence under home confinement, with digital surveillance.
They also petitioned that Bolsonaro be authorized to leave his home for medical treatment, saying he required regular treatment for pulmonary infections and other ailments.
Bolsonaro was found guilty of leading a plot aimed at maintaining his control after he failed to win the national vote to his political opponent, Lula.
Top judicial officials said that he had knowledge of a scheme which included plans to assassinate his opponent and his VP candidate, Alckmin, and to arrest and execute the presiding judge - the High Court judge who has been presiding over the former president's case.
The scheme was stopped because it failed to get the endorsement of the armed forces officials. The current president was took office without incident on the first day of 2023.
But a seven days after, on January 8th, numerous Bolsonaro supporters attacked and damaged official structures in the capital, Brasília.
The police took action and around fifteen hundred individuals were arrested.
The justices found that the protesters had been incited by him whose strategy, they said, was for the national armed forces to step in, reestablish control and return him to office.
At the period, Bolsonaro's lawyers called the decades-long sentence extremely harsh.
He was also barred from running for public office until the year 2060 - eight years later after the completion of his term.
The ex-leader called the legal proceedings a targeted investigation" and said it was intended to stop him running in the 2026 national vote.
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