Bolsonaro has been arrested after authorities concluded he posed a serious risk of fleeing while under domestic detention.
The ex-president was sentenced of planning a government overthrow in September and sentenced more than over two decades in prison, but he was staying under house arrest pending appeals.
Brazilian Supreme Court Justice Justice Moraes said the move to detain the elderly politician was a safety action after "new facts" were revealed.
This included trying to remove his tracking device and a invitation to a public vigil that could enable a potential flight.
In a document approving the custody, the judge said information from the centre monitoring Bolsonaro's house arrest suggested the one-time head of state's aim to disable the surveillance device to secure accomplishment in his flight.
This, it said, would be "facilitated by the disorder caused by the demonstration called by his son.
His child, FlƔvio, who holds office as a senator, called for a assembly of his backers near the former president's residence to take place on Saturday night.
FlƔvio Bolsonaro wrote on online platforms on the previous day: "Are you going to fight for your nation, or observe everything from your smartphone there on your settee? I urge you to struggle with us."
He said the gathering would be so backers could offer prayers for his health and for the restoration of democratic rule in our country."
Part of the judge's ruling was the potential of Bolsonaro's "relocation to diplomatic missions near the home, considering that the investigations revealed a record of organizing to seek refuge through a diplomatic representation", a declaration said.
The legal document underscores that the United States embassy in the national capital, the capital city, is positioned around 13km from Bolsonaro's home.
The former president's legal troubles have generated frustration from fellow populist conservative US President Trump, leading him to implement a fifty percent tax on goods coming from Brazil.
The former president is being kept in a Federal Police station in the capital and will experience a imprisonment assessment on the next day.
It was only on last Friday that the his legal team asked the High Court to allow him to serve his whole jail sentence under home confinement, with tracking devices.
They also petitioned that Bolsonaro be authorized to depart his residence for medical care, saying he required regular treatment for lung conditions and other illnesses.
The former president was convicted of leading a conspiracy aimed at keeping him in power after he was defeated in the 2022 election to his left-wing rival, Lula.
High Court judges said that he knew of a plan which involved plans to assassinate Lula and his vice-presidential running mate, his vice-presidential candidate, and to imprison and murder the presiding judge - the High Court judge who has been managing Bolsonaro's trial.
The conspiracy was thwarted because it couldn't obtain the support of the army and air force commanders. The current president was sworn in without incident on 1 January 2023.
But a seven days after, on 8 January, many Bolsonaro supporters invaded and destroyed official structures in the national capital, the capital city.
The security forces stepped in and around 1,500 people were detained.
The judges found that the protesters had been incited by him whose strategy, they said, was for the country's army to intervene, restore order and bring him back to power.
At the moment, Bolsonaro's lawyers called the over 27-year sentence extremely harsh.
He was also banned from campaigning for office until 2060 - eight years later after the completion of his term.
The ex-leader called the court case a targeted investigation" and said it was designed to prevent him competing in the next presidential race.
Elena es una escritora apasionada por la psicologĆa y los sueƱos, con experiencia en blogging y anĆ”lisis de temas existenciales.