Bolsonaro has been detained after authorities found he posed a concrete flight risk while under domestic detention.
The one-time leader was sentenced of orchestrating a military coup in September and sentenced more than a 27-year term in jail, but he was staying under confinement pending legal challenges.
Brazilian Supreme Court Justice the presiding justice said the decision to arrest the elderly politician was a safety action after "new facts" came to light.
This encompassed trying to remove his tracking device and a invitation to a supporters' gathering that could facilitate a potential flight.
In a filing authorising the detention, Justice Moraes said data from the centre monitoring Bolsonaro's house arrest suggested the one-time head of state's aim to disable the tracking monitor to guarantee victory in his getaway".
This, it said, would be assisted by the disorder caused by the protest called by his son.
His son, Flávio Bolsonaro, who works as a senator, called for a assembly of his backers near Bolsonaro's home to take place on the weekend.
The senator wrote on online platforms on Friday: "Are you going to fight for your homeland, or see it all from your smartphone there on your couch? I call on you to struggle with us."
He said the vigil would be so followers could offer prayers for his health and for the return of democracy in our nation."
Part of the judge's ruling was the chance of Bolsonaro's "relocation to foreign missions near the residence, considering that the inquiries revealed a history of organizing to ask for protection through a diplomatic representation", a statement said.
The court filing underscores that the American diplomatic mission in the national capital, Brazil's capital, is positioned around 8 miles from his dwelling.
The former president's legal troubles have provoked anger from fellow populist conservative US President Donald Trump, prompting him to implement a 50% tariff on Brazilian product imports.
He is being detained in a Federal Police station in Brasilia and will experience a custody hearing on Sunday.
It was only on the previous day that the former president's lawyers asked the High Court to permit him to fulfill his full incarceration period under home confinement, with electronic monitoring.
They also asked that Bolsonaro be authorized to exit his dwelling for medical care, saying he demanded ongoing care for lung conditions and other health problems.
He was determined responsible of heading a conspiracy aimed at maintaining his control after he lost the national vote to his ideological adversary, President Lula.
Top judicial officials said that he was aware of a scheme which encompassed plans to murder Lula and his vice-presidential running mate, his vice-presidential candidate, and to arrest and execute the presiding judge - the Supreme Court justice who has been presiding over the former president's case.
The plot was prevented because it couldn't obtain the backing of the armed forces officials. The current president was inaugurated without incident on 1 January 2023.
But a following week, on 8 January, thousands of his followers stormed and vandalised official structures in the federal district, the capital city.
The security forces intervened and around 1,500 people were detained.
The magistrates found that the demonstrators had been incited by Bolsonaro whose strategy, they said, was for the national armed forces to step in, bring back stability and bring him back to power.
At the period, his attorneys called the decades-long sentence unreasonably severe".
He was also banned from campaigning for office until 2060 - a decade minus two years after the completion of his term.
The one-time head of state called the trial a "witch hunt and said it was designed to prevent him running in the 2026 national vote.
Award-winning journalist with over a decade of experience covering international media and technology, known for insightful reporting and data-driven analysis.