Bolsonaro has been detained after authorities found he posed a serious risk of fleeing while under house arrest.
The ex-president was sentenced of planning a government overthrow in the ninth month and handed more than a 27-year term in incarceration, but he continued 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 fresh information emerged.
This encompassed attempting to break his ankle monitor and a invitation to a supporters' gathering that could enable a potential flight.
In a filing authorising the custody, the magistrate said data from the centre monitoring his home detention suggested the ex-president's "intention to break the surveillance device to ensure success in his flight.
This, it said, would be made easier by the chaos caused by the gathering called by his offspring.
His son, his son Flávio, who holds office as a legislator, called for a gathering of his supporters near the former president's residence to take place on the weekend.
Flávio Bolsonaro wrote on online platforms on last Friday: "Are you going to fight for your homeland, or observe everything from your mobile device there on your settee? I call on you to battle with us."
He said the vigil would be so supporters could offer prayers for his well-being and for the reestablishment of democratic governance in our country."
Part of the magistrate's determination was the potential of the former president's transfer to diplomatic missions near the dwelling, considering that the probes revealed a record of arranging to seek refuge through a diplomatic representation", a declaration said.
The legal document highlights that the United States embassy in the national capital, Brazil's capital, is positioned around approximately 13 kilometers from his dwelling.
The former president's legal troubles have provoked anger from fellow conservative nationalist United States President President Trump, leading him to impose a fifty percent tax 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 Sunday.
It was only on the previous day that the his legal team asked the Supreme Court to permit him to fulfill his full incarceration period under domestic detention, with digital surveillance.
They also requested that Bolsonaro be allowed to exit his dwelling for healthcare, saying he required regular treatment for pulmonary infections and other ailments.
He was determined responsible of leading a plot aimed at retaining his authority after he failed to win the presidential race to his left-wing rival, Lula.
Top judicial officials said that he was aware of a plan which involved plans to kill his opponent and his running partner, his vice-presidential candidate, and to arrest and execute Alexandre de Moraes - the High Court judge who has been overseeing Bolsonaro's trial.
The scheme was stopped because it failed to get the support of the army and air force commanders. Lula was sworn in without problem on January 1st, 2023.
But a following week, on the eighth of January, thousands of his followers invaded and destroyed government buildings in the capital, Brazil's capital.
The security forces intervened and around approximately 1,500 persons were arrested.
The magistrates found that the protesters had been incited by him whose strategy, they said, was for the Brazilian military to intervene, restore order and return him to office.
At the moment, his attorneys called the over 27-year sentence extremely harsh.
He was also banned from campaigning for office until 2060 - a decade minus two years after the end of his sentence.
The former president called the trial a "witch hunt and said it was aimed at blocking him running in the 2026 presidential election.
Elara is a tech journalist with a decade of experience covering software development and digital innovation trends.