Bolsonaro has been arrested after authorities determined he posed a concrete flight risk while under domestic detention.
The ex-president was convicted of planning a armed takeover in September and sentenced more than over two decades in jail, but he remained under home detention pending legal challenges.
High Court Judge Justice Moraes said the action to imprison the 70-year-old politician was a precautionary step after fresh information were revealed.
This involved seeking to disable his tracking device and a summons to a demonstration that could "allow for a potential flight.
In a document approving the arrest, Justice Moraes said intelligence from the facility tracking his home detention suggested the ex-president's "intention to break the tracking monitor to secure accomplishment in his escape.
This, it said, would be made easier by the confusion caused by the demonstration called by his offspring.
His son, Flávio, who holds office as a legislator, called for a meeting of his backers near his father's house to take place on the weekend.
Flávio Bolsonaro wrote on online platforms on Friday: Will you battle for your nation, or watch it all from your smartphone there on your sofa? I invite you to fight with us."
He said the gathering would be so backers could "pray for his health and for the return of democracy in our nation."
Part of the magistrate's decision was the chance of his "relocation to embassies near the dwelling, considering that the inquiries revealed a background of organizing to ask for protection through a consular facility", a declaration said.
The legal document highlights that the US embassy in the capital, Brazil's capital, is located around approximately 13 kilometers from Bolsonaro's home.
His judicial problems have provoked anger from fellow populist conservative American leader Donald Trump, causing him to enact a fifty percent tax on goods coming from Brazil.
He is being kept in a Federal Police station in Brazil's capital city and will undergo a imprisonment assessment on the next day.
It was only on last Friday that the his legal team asked the Top Court to allow him to complete his entire prison term under domestic detention, with digital surveillance.
They also requested that Bolsonaro be permitted to exit his dwelling for medical treatment, saying he required regular treatment for lung conditions and other ailments.
Bolsonaro was found guilty of leading a scheme aimed at maintaining his control after he lost the national vote to his ideological adversary, President Lula.
High Court judges said that he had knowledge of a scheme which encompassed plans to assassinate the current president and his vice-presidential running mate, Geraldo Alckmin, and to imprison and murder the presiding judge - the Supreme Court justice who has been overseeing Bolsonaro's trial.
The scheme was prevented because it didn't receive the backing of the military leaders. The current president was sworn in without issue on January 1st, 2023.
But a week later, on the eighth of January, many Bolsonaro supporters invaded and destroyed official structures in the federal district, the capital city.
The security forces intervened and around fifteen hundred individuals were detained.
The justices found that the rioters had been encouraged by him whose strategy, they said, was for the country's army to take action, restore order and reinstate his authority.
At the time, Bolsonaro's lawyers called the over 27-year sentence unreasonably severe".
He was also barred from seeking elected position until 2060 - a decade minus two years after the conclusion of his imprisonment.
The former president called the trial a "witch hunt and said it was designed to prevent him participating in the 2026 national vote.