Bolsonaro has been arrested after authorities concluded he posed a serious risk of fleeing while under home confinement.
The former head of state was convicted of planning a military coup in last fall and sentenced more than a 27-year term in jail, but he continued under confinement pending appeals.
High Court Judge Alexandre de Moraes said the decision to arrest the elderly politician was a preventative measure after "new facts" were revealed.
This involved seeking to disable his tracking device and a invitation to a demonstration that could enable a potential flight.
In a paperwork permitting the detention, the judge said information from the unit overseeing Bolsonaro's house arrest suggested the one-time head of state's plan to remove the tracking monitor to ensure success in his escape.
This, it said, would be "facilitated by the confusion caused by the demonstration called by his son.
His child, Flávio Bolsonaro, who works as a congressional representative, called for a meeting of his backers near the former president's residence to take place on Saturday night.
Flávio Bolsonaro wrote on online platforms on the previous day: Will you battle for your nation, or see it all from your smartphone there on your couch? I call on you to struggle with us."
He said the demonstration would be so supporters could "pray for his health and for the return of democracy in our country."
Part of Justice Moraes's determination was the possibility of the former president's transfer to foreign missions near the residence, considering that the investigations revealed a record of planning to ask for protection through a diplomatic representation", a announcement said.
The court filing emphasizes that the United States embassy in the national capital, Brazil's capital, is positioned around approximately 13 kilometers from the former president's residence.
Bolsonaro's legal woes have provoked anger from fellow conservative nationalist United States President Trump, leading him to implement a 50% tariff on goods coming from Brazil.
He is being held in a Federal Police station in the capital and will experience a detention review on Sunday.
It was only on last Friday that the ex-leader's attorneys asked the Top Court to allow him to fulfill his full incarceration period under home confinement, with digital surveillance.
They also requested that the former president be permitted to leave his home for medical treatment, saying he required ongoing care for respiratory ailments and other illnesses.
He was determined responsible of leading a scheme aimed at keeping him in power after he was defeated in the national vote to his political opponent, Luiz Inácio Lula da Silva.
Top judicial officials said that he had knowledge of a plan which included plans to kill the current president and his VP candidate, his vice-presidential candidate, and to imprison and murder Alexandre de Moraes - the Supreme Court justice who has been overseeing Bolsonaro's trial.
The plot was thwarted because it didn't receive the backing of the army and air force commanders. The current president was sworn in without problem on 1 January 2023.
But a following week, on the eighth of January, numerous his followers invaded and destroyed government buildings in the capital, Brasília.
The law enforcement stepped in and around fifteen hundred individuals were taken into custody.
The magistrates found that the demonstrators had been encouraged by him whose strategy, they said, was for the national armed forces to take action, restore order and bring him back to power.
At the moment, his attorneys called the 27 years and three months sentence "absurdly excessive.
He was also barred from campaigning for office until 2060 - eight years later after the conclusion of his imprisonment.
The ex-leader called the court case a targeted investigation" and said it was designed to prevent him participating in the 2026 presidential election.