Bolsonaro has been detained after authorities found he posed a definite escape threat while under domestic detention.
The former head of state was convicted of orchestrating a armed takeover in last fall and handed more than a 27-year term in jail, but he was staying under confinement pending legal challenges.
Top Judicial Official Justice Moraes said the action to imprison the septuagenarian politician was a safety action after "new facts" came to light.
This encompassed seeking to disable his ankle monitor and a invitation to a public vigil that could "allow for a possible escape.
In a paperwork permitting the custody, Justice Moraes said information from the centre monitoring the former president's confinement suggested the one-time head of state's aim to disable the surveillance device to secure accomplishment in his escape.
This, it said, would be made easier by the disorder caused by the gathering called by his offspring.
His son, Flávio Bolsonaro, who works as a senator, called for a gathering of his supporters near Bolsonaro's home to take place on Saturday evening.
His son wrote on social media on Friday: "Are you going to fight for your country, or watch it all from your smartphone there on your settee? I urge you to battle with us."
He said the gathering would be so followers could offer prayers for his physical condition and for the restoration of democratic rule in our country."
Part of the magistrate's determination was the possibility of Bolsonaro's move to diplomatic missions near the home, considering that the probes revealed a background of organizing to request asylum through a consular facility", a announcement said.
The court filing emphasizes that the United States embassy in the federal district, Brazil's capital, is positioned around approximately 13 kilometers from his dwelling.
The former president's legal troubles have generated frustration from fellow conservative nationalist US President Donald Trump, leading him to implement a half-rate duty on imports of Brazilian goods.
The former president is being kept in a federal law enforcement building in the capital and will undergo a custody hearing on Sunday.
It was only on Friday that the former president's lawyers asked the Supreme Court to authorize him to serve his whole jail sentence under home confinement, with electronic monitoring.
They also petitioned that he be authorized to leave his home for medical treatment, saying he needed frequent medical attention for lung conditions and other health problems.
Bolsonaro was found guilty of leading a plot aimed at retaining his authority after he was defeated in the 2022 election to his ideological adversary, Lula.
Supreme Court justices said that he was aware of a plot which included plans to assassinate his opponent and his running partner, Geraldo Alckmin, and to imprison and murder Justice Moraes - the Supreme Court justice who has been overseeing his judicial proceedings.
The scheme was thwarted because it failed to get the endorsement of the military leaders. The current president was inaugurated without issue on January 1st, 2023.
But a week later, on the eighth of January, thousands of his backers stormed and vandalised public facilities in the capital, Brazil's capital.
The police stepped in and around approximately 1,500 persons were arrested.
The justices found that the demonstrators had been provoked 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 moment, the legal team called the 27 years and three months sentence "absurdly excessive.
He was also banned from seeking elected position until twenty-sixty - eight years later after the end of his sentence.
The one-time head of state called the trial a targeted investigation" and said it was intended to stop him running in the 2026 presidential election.
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