Bolsonaro has been detained after authorities concluded he posed a serious risk of fleeing while under house arrest.
The former head of state was convicted of planning a armed takeover in September and sentenced more than 27 years in jail, but he remained under confinement pending court reviews.
Top Judicial Official the presiding justice said the move to detain the elderly politician was a preventative measure after recent developments emerged.
This encompassed trying to remove his electronic bracelet and a summons to a public vigil that could enable a potential flight.
In a filing authorising the custody, the magistrate said data from the unit overseeing the former president's confinement suggested the one-time head of state's aim to disable the surveillance device to ensure success in his getaway".
This, it said, would be made easier by the chaos caused by the protest called by his child.
His child, Flávio, who works as a legislator, called for a assembly of his supporters near the former president's residence to take place on the weekend.
Flávio Bolsonaro wrote on social media on Friday: "Are you going to fight for your country, or observe everything from your smartphone there on your couch? I urge you to battle with us."
He said the gathering would be so supporters could "pray for his health and for the reestablishment of democratic governance in our nation."
Part of Justice Moraes's decision was the possibility of his transfer to embassies near the home, considering that the investigations revealed a record of organizing to seek refuge through a diplomatic representation", a announcement said.
The judicial paperwork highlights that the United States embassy in the capital, the capital city, is located around approximately 13 kilometers from Bolsonaro's home.
The former president's legal troubles have provoked anger from fellow conservative nationalist American leader President Trump, prompting him to enact a half-rate duty on goods coming from Brazil.
Bolsonaro is being detained in a Federal Police station in Brasilia and will have a custody hearing on the next day.
It was only on last Friday that the his legal team asked the Supreme Court to allow him to complete his entire prison term under domestic detention, with digital surveillance.
They also requested that the former president be authorized to exit his dwelling for healthcare, saying he demanded frequent medical attention for pulmonary infections and other health problems.
He was determined responsible of orchestrating a scheme aimed at maintaining his control after he lost the 2022 election to his left-wing rival, Luiz Inácio Lula da Silva.
Top judicial officials said that he knew of a scheme which involved plans to assassinate Lula and his vice-presidential running mate, his vice-presidential candidate, and to arrest and execute Justice Moraes - the top judicial official who has been overseeing Bolsonaro's trial.
The scheme was prevented because it couldn't obtain the backing of the army and air force commanders. Lula was took office without incident on January 1st, 2023.
But a following week, on 8 January, thousands of Bolsonaro supporters stormed and vandalised government buildings in the national capital, Brazil's capital.
The security forces stepped in and around 1,500 people were arrested.
The judges found that the demonstrators had been incited by Bolsonaro whose strategy, they said, was for the Brazilian military to intervene, bring back stability and return him to office.
At the period, the legal team called the over 27-year sentence extremely harsh.
He was also barred from seeking elected position until twenty-sixty - eight years later after the end of his sentence.
The former president called the legal proceedings a "witch hunt and said it was designed to prevent him participating in the 2026 presidential election.
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