Bolsonaro has been arrested after authorities found he posed a concrete flight risk while under house arrest.
The former head of state was convicted of orchestrating a armed takeover in the ninth month and handed more than over two decades in incarceration, but he continued under house arrest pending legal challenges.
High Court Judge Justice Moraes said the action to imprison the 70-year-old politician was a safety action after recent developments emerged.
This included seeking to disable his ankle monitor and a call for a supporters' gathering that could enable a possible escape.
In a filing authorising the detention, the judge said intelligence from the facility tracking his home detention suggested the one-time head of state's "intention to break the tracking monitor to secure accomplishment in his escape.
This, it said, would be made easier by the disorder caused by the gathering called by his child.
His offspring, Flávio Bolsonaro, who holds office as a senator, called for a gathering of his backers near his father's house to take place on Saturday night.
The senator wrote on digital networks on last Friday: Do you plan to struggle for your country, or observe everything from your mobile device there on your couch? I call on you to struggle with us."
He said the gathering would be so supporters could "pray for his health and for the restoration of democratic rule in our nation."
Part of the judge's ruling was the chance of Bolsonaro's move to foreign missions near the dwelling, considering that the probes revealed a history of arranging to seek refuge through a embassy office", a declaration said.
The court filing emphasizes that the US embassy in the national capital, Brazil's capital, is positioned around 8 miles from his dwelling.
Bolsonaro's legal woes have drawn the ire of fellow right-wing populist United States President Donald Trump, causing him to implement a fifty percent tax on imports of Brazilian goods.
The former president is being kept in a Federal Police station in Brasilia and will experience a custody hearing on Sunday.
It was only on Friday that the his legal team asked the High Court to permit him to complete his entire prison term under domestic detention, with tracking devices.
They also requested that Bolsonaro be allowed to depart his residence for healthcare, saying he demanded frequent medical attention for respiratory ailments and other illnesses.
Bolsonaro was convicted of heading a scheme aimed at keeping him in power after he was defeated in the 2022 election to his ideological adversary, Luiz Inácio Lula da Silva.
High Court judges said that he was aware of a plot which encompassed plans to murder the current president and his VP candidate, Geraldo Alckmin, and to imprison and murder the presiding judge - the High Court judge who has been overseeing the former president's case.
The conspiracy was thwarted because it couldn't obtain the endorsement of the military leaders. Lula was sworn in without issue on 1 January 2023.
But a seven days after, on 8 January, thousands of his backers stormed and vandalised government buildings in the capital, BrasÃlia.
The law enforcement took action and around fifteen hundred individuals were taken into custody.
The justices found that the protesters had been provoked by Bolsonaro whose strategy, they said, was for the country's army to step in, reestablish control and bring him back to power.
At the time, Bolsonaro's lawyers called the over 27-year sentence extremely harsh.
He was also prohibited from campaigning for office until the year 2060 - eight years later after the conclusion of his imprisonment.
The one-time head of state called the legal proceedings a political persecution and said it was aimed at blocking him participating in the 2026 presidential election.
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