Bolsonaro has been arrested after authorities found he posed a serious risk of fleeing while under domestic detention.
The ex-president was sentenced of plotting a military coup in the ninth month and handed more than 27 years in jail, but he remained under confinement pending appeals.
Top Judicial Official Alexandre de Moraes said the move to detain the septuagenarian politician was a safety action after "new facts" emerged.
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 arrest, the magistrate said information from the unit overseeing Bolsonaro's house arrest suggested the ex-president's "intention to break the tracking monitor to guarantee victory in his flight.
This, it said, would be "facilitated by the disorder caused by the protest called by his offspring.
His son, his son Flávio, who holds office as a senator, called for a assembly of his followers near the former president's residence to take place on the weekend.
The senator wrote on digital networks on last Friday: Will you battle for your homeland, or see it all from your phone there on your couch? I urge you to struggle with us."
He said the vigil would be so supporters could "pray for his health and for the reestablishment of democratic governance in our country."
Part of the magistrate's ruling was the chance of Bolsonaro's transfer to embassies near the residence, considering that the inquiries revealed a history of organizing to request asylum through a diplomatic representation", a statement said.
The court filing highlights that the American diplomatic mission in the national capital, the capital city, is situated around 8 miles from Bolsonaro's home.
The former president's legal troubles have generated frustration from fellow conservative nationalist United States President President Trump, leading him to implement a half-rate duty on Brazilian product imports.
The former president is being detained in a national police facility in the capital and will experience a custody hearing on Sunday.
It was only on the previous day that the his legal team asked the High Court to permit him to complete his entire prison term under house arrest, with electronic monitoring.
They also requested that Bolsonaro be authorized to leave his home for medical care, saying he needed frequent medical attention for respiratory ailments and other ailments.
He was found guilty of heading a plot aimed at maintaining his control after he failed to win the presidential race to his political opponent, President Lula.
Supreme Court justices said that he had knowledge of a scheme which encompassed plans to murder his opponent and his running partner, his vice-presidential candidate, and to detain and kill Alexandre de Moraes - the top judicial official who has been managing Bolsonaro's trial.
The conspiracy was stopped because it failed to get the endorsement of the armed forces officials. The current president was inaugurated without problem on the first day of 2023.
But a following week, on 8 January, numerous his backers attacked and damaged government buildings in the national capital, the capital city.
The security forces intervened and around fifteen hundred individuals were detained.
The judges found that the rioters had been encouraged by the former president whose plan, they said, was for the national armed forces to step in, bring back stability and reinstate his authority.
At the time, his attorneys called the decades-long sentence "absurdly excessive.
He was also banned from seeking elected position until twenty-sixty - eight years later after the conclusion of his imprisonment.
The one-time head of state called the legal proceedings a targeted investigation" and said it was intended to stop him competing in the 2026 national vote.