Bolsonaro has been taken into custody after authorities found he posed a concrete flight risk while under domestic detention.
The ex-president was convicted of plotting a government overthrow in September and given more than over two decades in prison, but he remained under confinement pending appeals.
Top Judicial Official Alexandre de Moraes said the action to imprison the elderly politician was a safety action after "new facts" were revealed.
This included attempting to break his tracking device and a invitation to a demonstration that could facilitate a potential flight.
In a document approving the custody, Justice Moraes said intelligence from the unit overseeing his home detention suggested the ex-president's aim to disable the tracking monitor to guarantee victory in his flight.
This, it said, would be "facilitated by the chaos caused by the protest called by his offspring.
His child, FlĂ¡vio, who works as a congressional representative, called for a assembly of his followers near the former president's residence to take place on the weekend.
His son wrote on social media on Friday: "Are you going to fight for your nation, or watch it all from your smartphone there on your settee? I urge you to fight with us."
He said the gathering would be so followers could seek divine intervention for his health and for the restoration of democratic rule in our land."
Part of Justice Moraes's determination was the potential of Bolsonaro's move to diplomatic missions near the dwelling, considering that the probes revealed a history of organizing to ask for protection through a consular facility", a declaration said.
The judicial paperwork highlights that the US embassy in the capital, the capital city, is positioned around approximately 13 kilometers from Bolsonaro's home.
The former president's legal troubles have generated frustration from fellow right-wing populist US President President Trump, leading him to implement a half-rate duty on imports of Brazilian goods.
The former president is being kept in a national police facility in Brasilia and will undergo a imprisonment assessment on Sunday.
It was only on last Friday that the his legal team asked the High Court to allow him to complete his entire prison term under home confinement, with electronic monitoring.
They also petitioned that Bolsonaro be permitted to leave his home for medical care, saying he required ongoing care for respiratory ailments and other ailments.
Bolsonaro was convicted of leading a plot aimed at keeping him in power after he lost the 2022 election to his left-wing rival, Luiz InĂ¡cio Lula da Silva.
Top judicial officials said that he was aware of a plot which included plans to murder his opponent and his VP candidate, his vice-presidential candidate, and to imprison and murder the presiding judge - the top judicial official who has been presiding over the former president's case.
The scheme was thwarted because it couldn't obtain the backing of the armed forces officials. His successor was took office without issue on 1 January 2023.
But a following week, on 8 January, many Bolsonaro supporters attacked and damaged public facilities in the federal district, the capital city.
The law enforcement intervened and around 1,500 people were taken into custody.
The magistrates found that the demonstrators had been encouraged by him whose scheme, they said, was for the country's army to take action, bring back stability and bring him back to power.
At the time, his attorneys called the 27 years and three months sentence "absurdly excessive.
He was also banned from running for public office until twenty-sixty - a decade minus two years after the completion of his term.
The former president called the trial a "witch hunt and said it was aimed at blocking him participating in the 2026 national vote.
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