Bolsonaro has been arrested after authorities found he posed a serious risk of fleeing while under house arrest.
The former head of state was found guilty of planning a armed takeover in last fall and given more than over two decades in prison, but he continued under home detention pending legal challenges.
Top Judicial Official Justice Moraes said the move to detain the elderly politician was a precautionary step after "new facts" came to light.
This included attempting to break his ankle monitor and a summons to a public vigil that could "allow for a possible escape.
In a document approving the arrest, the judge said information from the facility tracking the former president's confinement suggested the ex-president's "intention to break the electronic ankle bracelet to ensure success in his escape.
This, it said, would be assisted by the chaos caused by the protest called by his offspring.
His offspring, Flávio, who holds office as a legislator, called for a assembly of his supporters near Bolsonaro's home to take place on Saturday night.
The senator wrote on online platforms on Friday: Will you battle for your nation, or watch it all from your mobile device there on your couch? I urge you to struggle with us."
He said the vigil would be so followers could seek divine intervention for his health and for the return of democracy in our land."
Part of the magistrate's determination was the chance of the former president's move to diplomatic missions near the home, considering that the probes revealed a record of organizing to seek refuge through a consular facility", a declaration said.
The legal document highlights that the American diplomatic mission in the national capital, Brasilia, is positioned around 13km from his dwelling.
His judicial problems have drawn the ire of fellow conservative nationalist United States President Donald Trump, prompting him to enact a fifty percent tax on Brazilian product imports.
Bolsonaro is being kept in a federal law enforcement building in the capital and will experience a detention review on the next day.
It was only on last Friday that the ex-leader's attorneys asked the Top Court to authorize him to complete his entire prison term under home confinement, with tracking devices.
They also requested that he be authorized to leave his home for medical care, saying he required ongoing care for lung conditions and other health problems.
Bolsonaro was found guilty of orchestrating a conspiracy aimed at maintaining his control after he failed to win the presidential race to his political opponent, Luiz Inácio Lula da Silva.
Top judicial officials said that he had knowledge of a plot which included plans to kill the current president and his vice-presidential running mate, Geraldo Alckmin, and to arrest and execute Justice Moraes - the top judicial official who has been managing his judicial proceedings.
The plot was thwarted because it didn't receive the endorsement of the army and air force commanders. Lula was took office without issue on the first day of 2023.
But a seven days after, on the eighth of January, many his followers invaded and destroyed official structures in the capital, BrasÃlia.
The law enforcement intervened and around fifteen hundred individuals were detained.
The justices found that the protesters had been encouraged by the former president whose strategy, they said, was for the Brazilian military to intervene, reestablish control and bring him back to power.
At the moment, the legal team called the decades-long sentence unreasonably severe".
He was also barred from campaigning for office until twenty-sixty - eight years after the conclusion of his imprisonment.
The one-time head of state called the trial a "witch hunt and said it was aimed at blocking him competing in the 2026 presidential election.
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