Bolsonaro has been arrested after authorities concluded he posed a serious risk of fleeing while under home confinement.
The ex-president was convicted of planning a government overthrow in the ninth month and given more than a 27-year term in prison, but he remained under house arrest pending appeals.
High Court Judge Alexandre de Moraes said the move to detain the 70-year-old politician was a safety action after "new facts" emerged.
This encompassed trying to remove his ankle monitor and a call for a public vigil that could facilitate a possible escape.
In a filing authorising the detention, the magistrate said intelligence from the facility tracking Bolsonaro's house arrest suggested the former leader's plan to remove the surveillance device to guarantee victory in his flight.
This, it said, would be made easier by the chaos caused by the gathering called by his offspring.
His child, his son Flávio, who works as a congressional representative, called for a gathering of his followers near his father's house to take place on Saturday evening.
The senator wrote on social media on the previous day: Will you battle for your homeland, or observe everything from your smartphone there on your sofa? I invite you to fight with us."
He said the vigil would be so backers could seek divine intervention for his health and for the return of democracy in our land."
Part of the judge's ruling was the chance of the former president's transfer to diplomatic missions near the residence, considering that the inquiries revealed a background of organizing to ask for protection through a embassy office", a declaration said.
The judicial paperwork emphasizes that the United States embassy in the national capital, Brasilia, is positioned around 13km from Bolsonaro's home.
Bolsonaro's legal woes have drawn the ire of fellow conservative nationalist United States President President Trump, causing him to implement a half-rate duty on goods coming from Brazil.
Bolsonaro is being kept in a Federal Police station in Brazil's capital city and will have a detention review on the following day.
It was only on last Friday that the ex-leader's attorneys asked the Supreme Court to allow him to complete his entire prison term under home confinement, with digital surveillance.
They also asked that the former president be authorized to exit his dwelling for medical care, saying he demanded ongoing care for pulmonary infections and other illnesses.
He was determined responsible of heading a conspiracy aimed at maintaining his control after he failed to win the 2022 election to his ideological adversary, Lula.
High Court judges said that he knew of a plot which encompassed plans to assassinate the current president and his running partner, Geraldo Alckmin, and to detain and kill Justice Moraes - the High Court judge who has been presiding over the former president's case.
The conspiracy was prevented because it failed to get the backing of the military leaders. His successor was inaugurated without incident on January 1st, 2023.
But a seven days after, on 8 January, thousands of his followers invaded and destroyed public facilities in the capital, the capital city.
The law enforcement intervened and around approximately 1,500 persons were detained.
The judges found that the demonstrators had been provoked by the former president whose plan, they said, was for the national armed forces to step in, restore order and reinstate his authority.
At the time, the legal team called the 27 years and three months sentence unreasonably severe".
He was also prohibited from campaigning for office until 2060 - a decade minus two years after the conclusion of his imprisonment.
The ex-leader called the court case a targeted investigation" and said it was designed to prevent him running in the next presidential race.
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