Bolsonaro has been detained after authorities determined he posed a concrete flight risk while under domestic detention.
The former head of state was convicted of orchestrating a military coup in September and sentenced more than 27 years in incarceration, but he continued under confinement pending legal challenges.
High Court Judge Justice Moraes said the move to detain the elderly politician was a preventative measure after "new facts" came to light.
This encompassed seeking to disable his ankle monitor and a call for a public vigil that could enable a chance to flee".
In a document approving the custody, Justice Moraes said data from the centre monitoring Bolsonaro's house arrest suggested the former leader's aim to disable the surveillance device to guarantee victory in his getaway".
This, it said, would be made easier by the chaos caused by the gathering called by his offspring.
His child, Flávio Bolsonaro, who holds office as a senator, called for a assembly of his supporters near his father's house to take place on the weekend.
Flávio Bolsonaro wrote on social media on the previous day: "Are you going to fight for your homeland, or watch it all from your phone there on your couch? I urge you to fight with us."
He said the gathering would be so supporters could "pray for his physical condition and for the return of democracy in our country."
Part of the magistrate's decision was the potential of his move to foreign missions near the residence, considering that the inquiries revealed a history of arranging to seek refuge through a diplomatic representation", a declaration said.
The legal document highlights that the US embassy in the federal district, the capital city, is positioned around 13km from the former president's residence.
The former president's legal troubles have generated frustration from fellow conservative nationalist US President President Trump, prompting him to enact a 50% tariff on goods coming from Brazil.
The former president is being held in a federal law enforcement building in Brazil's capital city and will have a imprisonment assessment on the next day.
It was only on Friday that the his legal team asked the Supreme Court to authorize him to complete his entire prison term under house arrest, with electronic monitoring.
They also asked that Bolsonaro be authorized to depart his residence for medical care, saying he needed frequent medical attention for pulmonary infections and other health problems.
He was determined responsible of orchestrating a plot aimed at maintaining his control after he failed to win the 2022 election to his left-wing rival, Luiz Inácio Lula da Silva.
Supreme Court justices said that he knew of a plot which included plans to murder Lula and his running partner, Alckmin, and to detain and kill Alexandre de Moraes - the High Court judge who has been overseeing the former president's case.
The plot was stopped because it didn't receive the backing of the military leaders. The current president was sworn in without incident on January 1st, 2023.
But a week later, on the eighth of January, many his followers attacked and damaged official structures in the federal district, Brasília.
The police intervened and around approximately 1,500 persons were arrested.
The justices found that the rioters had been provoked by the former president whose scheme, they said, was for the country's army to take action, restore order and reinstate his authority.
At the time, Bolsonaro's lawyers called the over 27-year sentence unreasonably severe".
He was also barred from seeking elected position until the year 2060 - eight years after the end of his sentence.
The one-time head of state called the legal proceedings a "witch hunt and said it was intended to stop him competing in the next presidential race.
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