Bolsonaro has been detained after authorities found he posed a serious risk of fleeing while under domestic detention.
The former head of state was convicted of plotting a government overthrow in September and sentenced more than a 27-year term in prison, but he was staying under house arrest pending legal challenges.
High Court Judge Justice Moraes said the move to detain the 70-year-old politician was a preventative measure after "new facts" came to light.
This involved attempting to break his electronic bracelet and a invitation to a supporters' gathering that could enable a possible escape.
In a document approving the custody, the magistrate said intelligence from the centre monitoring the former president's confinement suggested the former leader's aim to disable the electronic ankle bracelet to ensure success in his getaway".
This, it said, would be made easier by the disorder caused by the gathering called by his son.
His son, Flávio Bolsonaro, who works as a legislator, called for a gathering of his followers near Bolsonaro's home to take place on Saturday night.
The senator wrote on social media on the previous day: "Are you going to fight for your homeland, or observe everything from your mobile device there on your couch? I call on you to struggle with us."
He said the demonstration would be so supporters could seek divine intervention for his health and for the reestablishment of democratic governance in our land."
Part of the magistrate's decision was the potential of the former president's "relocation to foreign missions near the residence, considering that the investigations revealed a record of arranging to seek refuge through a diplomatic representation", a announcement said.
The legal document highlights that the American diplomatic mission in the national capital, Brazil's capital, is located around 8 miles from Bolsonaro's home.
The former president's legal troubles have provoked anger from fellow conservative nationalist United States President Donald Trump, leading him to enact a fifty percent tax on Brazilian product imports.
Bolsonaro is being detained in a federal law enforcement building in Brazil's capital city and will have a detention review on Sunday.
It was only on the previous day that the his legal team asked the High Court to permit him to serve his whole jail sentence under house arrest, with digital surveillance.
They also asked that he be authorized to leave his home for healthcare, saying he demanded ongoing care for lung conditions and other ailments.
Bolsonaro was found guilty of orchestrating a plot aimed at keeping him in power after he was defeated in the national vote to his political opponent, Luiz Inácio Lula da Silva.
Top judicial officials said that he knew of a plot which involved plans to kill the current president and his vice-presidential running mate, Geraldo Alckmin, and to detain and kill Alexandre de Moraes - the top judicial official who has been overseeing Bolsonaro's trial.
The plot was thwarted because it couldn't obtain the endorsement of the army and air force commanders. The current president was sworn in without issue on the first day of 2023.
But a week later, on January 8th, numerous Bolsonaro supporters invaded and destroyed government buildings in the federal district, the capital city.
The law enforcement stepped in and around approximately 1,500 persons were arrested.
The justices found that the protesters had been provoked by the former president whose scheme, they said, was for the national armed forces to take action, bring back stability and return him to office.
At the time, his attorneys called the decades-long sentence "absurdly excessive.
He was also prohibited from running for public office until 2060 - eight years later after the conclusion of his imprisonment.
The ex-leader called the trial a political persecution and said it was intended to stop him participating in the next presidential race.
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