Bolsonaro has been arrested after authorities concluded he posed a definite escape threat while under domestic detention.
The former head of state was convicted of plotting a government overthrow in last fall and handed more than a 27-year term in prison, but he continued under home detention pending legal challenges.
High Court Judge Alexandre de Moraes said the move to detain the 70-year-old politician was a preventative measure after recent developments came to light.
This involved attempting to break his electronic bracelet and a summons to a supporters' gathering that could enable a potential flight.
In a filing authorising the custody, Justice Moraes said data from the facility tracking Bolsonaro's house arrest suggested the one-time head of state's plan to remove the surveillance device to secure accomplishment in his getaway".
This, it said, would be assisted by the confusion caused by the demonstration called by his son.
His son, Flávio Bolsonaro, who holds office as a senator, called for a assembly of his backers near his father's house to take place on Saturday night.
Flávio Bolsonaro wrote on digital networks on Friday: "Are you going to fight for your country, or watch it all from your smartphone there on your settee? I invite you to struggle with us."
He said the vigil would be so supporters could seek divine intervention for his health and for the restoration of democratic rule in our land."
Part of the magistrate's determination was the chance of Bolsonaro's "relocation to diplomatic missions near the dwelling, considering that the inquiries revealed a record of organizing to request asylum through a consular facility", a statement said.
The judicial paperwork emphasizes that the US embassy in the federal district, Brasilia, is situated around 8 miles from Bolsonaro's home.
His judicial problems have provoked anger from fellow conservative nationalist American leader Donald Trump, prompting him to implement a half-rate duty on imports of Brazilian goods.
The former president is being detained in a national police facility in Brazil's capital city and will experience a detention review on the following day.
It was only on the previous day that the former president's lawyers asked the Top Court to allow him to complete his entire prison term under domestic detention, with electronic monitoring.
They also asked that Bolsonaro be permitted to depart his residence for healthcare, saying he needed frequent medical attention for respiratory ailments and other illnesses.
He was determined responsible of orchestrating a plot aimed at keeping him in power after he failed to win the presidential race to his political opponent, President Lula.
Top judicial officials said that he knew of a plot which included plans to murder Lula and his VP candidate, his vice-presidential candidate, and to arrest and execute Justice Moraes - the top judicial official who has been managing his judicial proceedings.
The scheme was thwarted because it didn't receive the backing of the army and air force commanders. Lula was sworn in without issue on 1 January 2023.
But a week later, on the eighth of January, thousands of his backers attacked and damaged government buildings in the federal district, Brasília.
The police took action and around 1,500 people were detained.
The justices found that the protesters had been encouraged by Bolsonaro whose scheme, they said, was for the national armed forces to take action, restore order and return him to office.
At the moment, the legal team called the 27 years and three months sentence unreasonably severe".
He was also banned from running for public office until 2060 - a decade minus two years after the completion of his term.
The ex-leader called the trial a targeted investigation" and said it was aimed at blocking him participating in the 2026 presidential election.