Bolsonaro has been taken into custody after authorities concluded he posed a serious risk of fleeing while under domestic detention.
The ex-president was convicted of planning a armed takeover in last fall and given more than 27 years in incarceration, but he continued under confinement pending appeals.
High Court Judge the presiding justice said the action to imprison the 70-year-old politician was a preventative measure after fresh information were revealed.
This included trying to remove his ankle monitor and a invitation to a supporters' gathering that could "allow for a chance to flee".
In a filing authorising the custody, the magistrate said information from the facility tracking the former president's confinement suggested the one-time head of state's aim to disable the surveillance device to secure accomplishment in his flight.
This, it said, would be made easier by the confusion caused by the gathering called by his child.
His offspring, his son Flávio, who works as a congressional representative, called for a gathering of his followers near the former president's residence to take place on Saturday evening.
His son wrote on digital networks on Friday: "Are you going to fight for your country, or observe everything from your mobile device there on your settee? I invite you to fight with us."
He said the demonstration would be so backers could offer prayers for his health and for the restoration of democratic rule in our country."
Part of the judge's ruling was the chance of his move to diplomatic missions near the dwelling, considering that the inquiries revealed a background of organizing to seek refuge through a embassy office", a statement said.
The legal document underscores that the United States embassy in the federal district, Brazil's capital, is positioned around 13km from the former president's residence.
Bolsonaro's legal woes have generated frustration from fellow conservative nationalist United States President Donald Trump, leading him to enact a fifty percent tax on imports of Brazilian goods.
The former president is being detained in a Federal Police station in the capital and will experience a detention review on the next day.
It was only on last Friday that the his legal team asked the Supreme Court to permit him to complete his entire prison term under domestic detention, with digital surveillance.
They also petitioned that the former president be allowed to depart his residence for healthcare, saying he needed ongoing care for pulmonary infections and other illnesses.
He was convicted of orchestrating a scheme aimed at maintaining his control after he failed to win the national vote to his left-wing rival, Luiz Inácio Lula da Silva.
High Court judges said that he had knowledge of a scheme which encompassed plans to kill Lula and his vice-presidential running mate, Geraldo Alckmin, and to arrest and execute Alexandre de Moraes - the High Court judge who has been managing his judicial proceedings.
The scheme was thwarted because it failed to get the backing of the army and air force commanders. Lula was took office without problem on the first day of 2023.
But a week later, on January 8th, numerous Bolsonaro supporters stormed and vandalised government buildings in the capital, BrasÃlia.
The law enforcement took action and around 1,500 people were detained.
The justices found that the demonstrators had been incited by the former president whose plan, they said, was for the Brazilian military to step in, bring back stability and bring him back to power.
At the period, the legal team called the 27 years and three months sentence extremely harsh.
He was also banned from running for public office until 2060 - eight years later after the completion of his term.
The ex-leader called the court case a targeted investigation" and said it was aimed at blocking him participating in the 2026 presidential election.
Elara Vance is a technology strategist with over a decade of experience in IT consulting, specializing in digital transformation and cybersecurity solutions.