Bolsonaro has been taken into custody after authorities determined he posed a serious risk of fleeing while under domestic detention.
The former head of state was sentenced of orchestrating a military coup in last fall and handed more than over two decades in incarceration, but he was staying under house arrest pending appeals.
High Court Judge the presiding justice said the move to detain the 70-year-old politician was a safety action after recent developments emerged.
This encompassed seeking to disable his tracking device and a call for a supporters' gathering that could facilitate a potential flight.
In a document approving the detention, the judge said information from the unit overseeing the former president's confinement suggested the one-time head of state's plan to remove the surveillance device to secure accomplishment in his flight.
This, it said, would be "facilitated by the confusion caused by the gathering called by his son.
His child, Flávio Bolsonaro, who serves as a congressional representative, called for a gathering of his followers near the former president's residence to take place on Saturday night.
The senator wrote on digital networks on last Friday: Do you plan to struggle for your homeland, or watch it all from your smartphone there on your couch? I urge you to struggle with us."
He said the gathering would be so backers could offer prayers for his well-being and for the reestablishment of democratic governance in our nation."
Part of the magistrate's determination was the chance of his transfer to diplomatic missions near the home, considering that the probes revealed a background of planning to request asylum through a embassy office", a announcement said.
The court filing emphasizes that the American diplomatic mission in the capital, the capital city, is positioned around approximately 13 kilometers from Bolsonaro's home.
Bolsonaro's legal woes have generated frustration from fellow populist conservative US President Trump, causing him to enact a half-rate duty on imports of Brazilian goods.
The former president is being kept in a Federal Police station in the capital and will have a detention review on the following day.
It was only on last Friday that the former president's lawyers asked the Top Court to authorize him to fulfill his full incarceration period under house arrest, with electronic monitoring.
They also asked that he be allowed to leave his home for medical treatment, saying he required ongoing care for lung conditions and other ailments.
Bolsonaro was determined responsible of heading a plot aimed at retaining his authority after he lost the presidential race to his political opponent, President Lula.
High Court judges said that he had knowledge of a scheme which encompassed plans to assassinate his opponent and his vice-presidential running mate, his vice-presidential candidate, and to imprison and murder Alexandre de Moraes - the Supreme Court justice who has been managing the former president's case.
The plot was prevented because it failed to get the support of the military leaders. Lula was sworn in without problem on January 1st, 2023.
But a following week, on 8 January, numerous Bolsonaro supporters stormed and vandalised government buildings in the federal district, the capital city.
The police stepped in and around 1,500 people were arrested.
The justices found that the demonstrators had been incited by Bolsonaro whose scheme, they said, was for the country's army to take action, reestablish control and bring him back to power.
At the time, his attorneys called the over 27-year sentence unreasonably severe".
He was also banned from running for public office until twenty-sixty - eight years later after the end of his sentence.
The ex-leader called the legal proceedings a political persecution and said it was designed to prevent him participating in the next presidential race.