Bolsonaro has been arrested after authorities found he posed a concrete flight risk while under home confinement.
The ex-president was convicted of plotting a armed takeover in September and handed more than a 27-year term in jail, but he continued under confinement pending legal challenges.
Brazilian Supreme Court Justice Alexandre de Moraes said the action to imprison the elderly politician was a precautionary step after recent developments came to light.
This encompassed seeking to disable his electronic bracelet and a summons to a supporters' gathering that could enable a chance to flee".
In a paperwork permitting the custody, the magistrate said data from the facility tracking Bolsonaro's house arrest suggested the former leader's aim to disable the surveillance device to ensure success in his flight.
This, it said, would be assisted by the confusion caused by the gathering called by his offspring.
His son, Flávio Bolsonaro, who works as a congressional representative, called for a assembly of his followers near Bolsonaro's home 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 phone there on your sofa? I invite you to struggle with us."
He said the demonstration would be so supporters could seek divine intervention for his physical condition and for the restoration of democratic rule in our country."
Part of Justice Moraes's ruling was the possibility of the former president's "relocation to diplomatic missions near the dwelling, considering that the investigations revealed a record of arranging to ask for protection through a embassy office", a announcement said.
The legal document emphasizes that the American diplomatic mission in the capital, Brasilia, is positioned around 13km from his dwelling.
The former president's legal troubles have generated frustration from fellow conservative nationalist US President Trump, causing him to implement a fifty percent tax on imports of Brazilian goods.
Bolsonaro is being kept in a federal law enforcement building in Brasilia and will experience a detention review on the following day.
It was only on last Friday that the his legal team asked the Supreme Court to allow him to complete his entire prison term under home confinement, with tracking devices.
They also petitioned that the former president be authorized to leave his home for medical care, saying he demanded ongoing care for lung conditions and other health problems.
The former president was found guilty of orchestrating a conspiracy aimed at keeping him in power after he was defeated in the presidential race to his left-wing rival, Lula.
Top judicial officials said that he had knowledge of a scheme which included plans to assassinate Lula and his running partner, Alckmin, and to detain and kill Alexandre de Moraes - the High Court judge who has been overseeing his judicial proceedings.
The conspiracy was thwarted because it didn't receive the support of the army and air force commanders. Lula was took office without incident on January 1st, 2023.
But a following week, on 8 January, numerous his backers stormed and vandalised official structures in the national capital, the capital city.
The law enforcement intervened and around 1,500 people were arrested.
The judges found that the rioters had been encouraged by him whose plan, they said, was for the Brazilian military to intervene, restore order and reinstate his authority.
At the moment, the legal team called the 27 years and three months sentence unreasonably severe".
He was also barred from running for public office until 2060 - eight years later after the end of his sentence.
The ex-leader called the trial a targeted investigation" and said it was designed to prevent him running in the 2026 presidential election.