Bolsonaro has been detained after authorities found he posed a serious risk of fleeing while under domestic detention.
The one-time leader was found guilty of planning a government overthrow in September and sentenced more than over two decades in jail, but he was staying under home detention pending court reviews.
High Court Judge Justice Moraes said the decision to arrest the elderly politician was a preventative measure after recent developments came to light.
This encompassed seeking to disable his tracking device and a invitation to a public vigil that could facilitate a possible escape.
In a paperwork permitting the detention, the magistrate said intelligence from the facility tracking his home detention suggested the one-time head of state's plan to remove the electronic ankle bracelet to guarantee victory in his escape.
This, it said, would be assisted by the chaos caused by the gathering called by his child.
His son, Flávio, who serves as a congressional representative, called for a meeting of his backers near the former president's residence to take place on Saturday evening.
His son wrote on digital networks on last Friday: Will you battle for your country, or see it all from your mobile device there on your couch? I invite you to fight with us."
He said the vigil would be so followers could "pray for his physical condition and for the return of democracy in our land."
Part of the magistrate's ruling was the chance of Bolsonaro's transfer to foreign missions near the dwelling, considering that the inquiries revealed a background of organizing to seek refuge through a diplomatic representation", a announcement said.
The court filing underscores that the US embassy in the national capital, the capital city, is positioned around approximately 13 kilometers from Bolsonaro's home.
The former president's legal troubles have drawn the ire of fellow right-wing populist US President President Trump, causing him to enact a fifty percent tax on Brazilian product imports.
The former president is being detained in a Federal Police station in Brazil's capital city and will have a custody hearing on the next day.
It was only on the previous day that the his legal team asked the Top Court to permit him to fulfill his full incarceration period under home confinement, with digital surveillance.
They also requested that the former president be permitted to leave his home for healthcare, saying he demanded ongoing care for pulmonary infections and other illnesses.
The former president was convicted of leading a conspiracy aimed at retaining his authority after he failed to win the presidential race to his left-wing rival, Lula.
Supreme Court justices said that he had knowledge of a scheme which encompassed plans to kill his opponent and his vice-presidential running mate, Geraldo Alckmin, and to imprison and murder the presiding judge - the High Court judge who has been overseeing Bolsonaro's trial.
The plot was prevented because it couldn't obtain the support of the army and air force commanders. Lula was inaugurated without issue on the first day of 2023.
But a following week, on 8 January, thousands of Bolsonaro supporters invaded and destroyed government buildings in the federal district, Brazil's capital.
The police took action and around 1,500 people were detained.
The justices found that the protesters had been incited by the former president whose strategy, they said, was for the Brazilian military to step in, bring back stability and return him to office.
At the time, his attorneys called the over 27-year sentence extremely harsh.
He was also barred from seeking elected position until the year 2060 - eight years after the end of his sentence.
The former president called the legal proceedings a political persecution and said it was aimed at blocking him participating in the 2026 presidential election.