Bolsonaro has been taken into custody after authorities concluded he posed a concrete flight risk while under house arrest.
The one-time leader was found guilty of planning a armed takeover in September and given more than over two decades in prison, but he was staying under house arrest pending legal challenges.
High Court Judge Justice Moraes said the action to imprison the septuagenarian politician was a safety action after recent developments emerged.
This included seeking to disable his tracking device and a call for a supporters' gathering that could facilitate a possible escape.
In a paperwork permitting the arrest, the magistrate said information from the facility tracking his home detention suggested the former leader's "intention to break the tracking monitor to secure accomplishment in his escape.
This, it said, would be assisted by the confusion caused by the protest called by his son.
His son, his son Flávio, who works as a legislator, called for a meeting of his backers near the former president's residence to take place on Saturday night.
His son wrote on social media on the previous day: "Are you going to fight for your homeland, or observe everything from your smartphone there on your settee? I invite you to battle with us."
He said the vigil would be so followers could "pray for his physical condition and for the reestablishment of democratic governance in our nation."
Part of the magistrate's determination was the chance of his move to foreign missions near the dwelling, considering that the investigations revealed a history of organizing to seek refuge through a diplomatic representation", a declaration said.
The court filing emphasizes that the American diplomatic mission in the capital, Brazil's capital, is located around 8 miles from his dwelling.
His judicial problems have drawn the ire of fellow conservative nationalist American leader President Trump, leading him to implement a fifty percent tax on imports of Brazilian goods.
He is being detained in a federal law enforcement building in Brazil's capital city and will undergo a custody hearing on Sunday.
It was only on the previous day that the ex-leader's attorneys asked the High Court to permit him to fulfill his full incarceration period under house arrest, with electronic monitoring.
They also petitioned that he be authorized to exit his dwelling for medical care, saying he required ongoing care for lung conditions and other health problems.
Bolsonaro was convicted of heading a plot aimed at maintaining his control after he lost the 2022 election to his ideological adversary, President Lula.
High Court judges said that he had knowledge of a plot which included plans to assassinate Lula and his VP candidate, Geraldo Alckmin, and to detain and kill Alexandre de Moraes - the High Court judge who has been presiding over the former president's case.
The plot was thwarted because it couldn't obtain the support of the army and air force commanders. Lula was took office without incident on January 1st, 2023.
But a following week, on 8 January, many his backers invaded and destroyed public facilities in the national capital, Brasília.
The police stepped in and around 1,500 people were taken into custody.
The justices found that the protesters had been encouraged by him whose strategy, they said, was for the Brazilian military to step in, reestablish control and bring him back to power.
At the time, his attorneys called the 27 years and three months sentence unreasonably severe".
He was also barred from campaigning for office until the year 2060 - eight years after the end of his sentence.
The former president called the court case a political persecution and said it was intended to stop him running in the 2026 presidential election.
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