Bolsonaro has been detained after authorities found he posed a concrete flight risk while under home confinement.
The former head of state was convicted of orchestrating a armed takeover in the ninth month and handed more than 27 years in incarceration, but he remained under home detention pending court reviews.
High Court Judge Justice Moraes said the move to detain the elderly politician was a preventative measure after fresh information emerged.
This involved seeking to disable his ankle monitor and a call for a supporters' gathering that could "allow for a possible escape.
In a paperwork permitting the detention, the judge said data from the facility tracking his home detention suggested the ex-president's "intention to break the tracking monitor to guarantee victory in his escape.
This, it said, would be made easier by the confusion caused by the demonstration called by his offspring.
His offspring, his son Flávio, who serves as a senator, called for a meeting of his followers near the former president's residence to take place on Saturday evening.
The senator 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 urge you to struggle with us."
He said the demonstration would be so supporters could seek divine intervention for his well-being and for the reestablishment of democratic governance in our nation."
Part of Justice Moraes's determination was the potential of Bolsonaro's move to embassies near the residence, considering that the probes revealed a record of organizing to seek refuge through a diplomatic representation", a declaration said.
The court filing highlights that the US embassy in the national capital, Brazil's capital, is situated around 13km from his dwelling.
Bolsonaro's legal woes have provoked anger from fellow right-wing populist US President Trump, leading him to impose a 50% tariff on imports of Brazilian goods.
He is being kept in a Federal Police station in Brazil's capital city and will have a imprisonment assessment on the next day.
It was only on the previous day that the former president's lawyers asked the Supreme Court to allow him to complete his entire prison term under house arrest, with tracking devices.
They also requested that he be allowed to depart his residence for medical treatment, saying he demanded ongoing care for respiratory ailments and other ailments.
The former president was found guilty of heading a scheme aimed at maintaining his control after he failed to win the 2022 election to his ideological adversary, President Lula.
High Court judges said that he was aware of a scheme which involved plans to assassinate the current president and his running partner, his vice-presidential candidate, and to imprison and murder the presiding judge - the Supreme Court justice who has been managing the former president's case.
The scheme was thwarted because it couldn't obtain the endorsement of the army and air force commanders. His successor was inaugurated without issue on the first day of 2023.
But a seven days after, on 8 January, thousands of his backers stormed and vandalised official structures in the federal district, BrasÃlia.
The security forces stepped in and around 1,500 people were detained.
The judges found that the demonstrators had been provoked by him whose strategy, they said, was for the country's army to take action, restore order and reinstate his authority.
At the period, his attorneys called the 27 years and three months sentence extremely harsh.
He was also prohibited from running for public office until twenty-sixty - eight years later after the conclusion of his imprisonment.
The one-time head of state called the legal proceedings a "witch hunt and said it was aimed at blocking him competing in the 2026 national vote.
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