Bolsonaro has been detained after authorities determined he posed a definite escape threat while under domestic detention.
The ex-president was found guilty of orchestrating a military coup in last fall and sentenced more than a 27-year term in jail, but he continued under home detention pending appeals.
Brazilian Supreme Court Justice the presiding justice said the move to detain the elderly politician was a safety action after recent developments came to light.
This involved seeking to disable his electronic bracelet and a call for a demonstration that could "allow for a chance to flee".
In a document approving the arrest, the magistrate said intelligence from the facility tracking his home detention suggested the one-time head of state's "intention to break the electronic ankle bracelet to ensure success in his flight.
This, it said, would be made easier by the chaos caused by the gathering called by his son.
His child, Flávio, who serves as a congressional representative, called for a assembly of his backers near Bolsonaro's home to take place on Saturday evening.
His son wrote on digital networks on last Friday: Do you plan to struggle for your country, or observe everything from your phone there on your sofa? I call on you to battle with us."
He said the vigil would be so supporters could offer prayers for his health and for the restoration of democratic rule in our nation."
Part of the judge's ruling was the possibility of his move to foreign missions near the dwelling, considering that the inquiries revealed a record of planning to request asylum through a embassy office", a statement said.
The court filing emphasizes that the United States embassy in the capital, Brazil's capital, is positioned around 13km from Bolsonaro's home.
Bolsonaro's legal woes have generated frustration from fellow conservative nationalist United States President President Trump, leading him to implement a 50% tariff on imports of Brazilian goods.
Bolsonaro is being held in a national police facility in Brasilia and will experience a detention review on the next day.
It was only on Friday that the ex-leader's attorneys asked the Supreme Court to permit him to fulfill his full incarceration period under domestic detention, with electronic monitoring.
They also requested that the former president be permitted to exit his dwelling for healthcare, saying he required ongoing care for lung conditions and other illnesses.
The former president was convicted of heading a scheme aimed at keeping him in power after he failed to win the presidential race to his ideological adversary, President Lula.
Top judicial officials said that he was aware of a plan which involved plans to assassinate his opponent and his VP candidate, Geraldo Alckmin, and to detain and kill the presiding judge - the High Court judge who has been overseeing the former president's case.
The conspiracy was thwarted because it didn't receive the backing of the army and air force commanders. The current president was sworn in without incident on 1 January 2023.
But a week later, on 8 January, many Bolsonaro supporters invaded and destroyed official structures in the federal district, Brazil's capital.
The security forces took action and around approximately 1,500 persons were arrested.
The magistrates found that the rioters had been provoked by the former president whose scheme, they said, was for the Brazilian military to intervene, bring back stability and return him to office.
At the moment, the legal team called the over 27-year sentence extremely harsh.
He was also prohibited from campaigning for office until 2060 - eight years later after the completion of his term.
The former president called the trial a targeted investigation" and said it was intended to stop him participating in the 2026 presidential election.
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