Bolsonaro has been taken into custody after authorities concluded he posed a definite escape threat while under domestic detention.
The former head of state was convicted of plotting a government overthrow in last fall and given more than over two decades in prison, but he remained under confinement pending appeals.
Top Judicial Official Alexandre de Moraes said the decision to arrest the elderly politician was a preventative measure after "new facts" came to light.
This included attempting to break his ankle monitor and a call for a demonstration that could facilitate a possible escape.
In a filing authorising the arrest, the judge said information from the centre monitoring his home detention suggested the former leader's aim to disable the tracking monitor to ensure success in his getaway".
This, it said, would be assisted by the confusion caused by the protest called by his child.
His son, Flávio, who holds office as a senator, called for a meeting of his followers near Bolsonaro's home to take place on Saturday evening.
Flávio Bolsonaro wrote on online platforms on Friday: Do you plan to struggle for your country, or watch it all from your phone there on your sofa? I urge you to fight with us."
He said the vigil would be so followers could offer prayers for his physical condition and for the restoration of democratic rule in our nation."
Part of Justice Moraes's determination was the chance of the former president's "relocation to foreign missions near the residence, considering that the investigations revealed a record of organizing to seek refuge through a embassy office", a announcement said.
The judicial paperwork emphasizes that the United States embassy in the capital, Brazil's capital, is located around 13km from Bolsonaro's home.
His judicial problems have provoked anger from fellow right-wing populist American leader President Trump, causing him to implement a 50% tariff on Brazilian product imports.
The former president is being kept in a federal law enforcement building in Brazil's capital city and will undergo a detention review on the next day.
It was only on Friday that the former president's lawyers asked the High Court to permit him to serve his whole jail sentence under domestic detention, with tracking devices.
They also asked that he be allowed to exit his dwelling for medical care, saying he required regular treatment for pulmonary infections and other ailments.
He was found guilty of leading a conspiracy aimed at maintaining his control after he lost the national vote to his left-wing rival, President Lula.
Top judicial officials said that he had knowledge of a plot which included plans to assassinate the current president and his vice-presidential running mate, Alckmin, and to detain and kill Justice Moraes - the High Court judge who has been overseeing his judicial proceedings.
The conspiracy was stopped because it couldn't obtain the support of the military leaders. The current president was inaugurated without problem on 1 January 2023.
But a following week, on the eighth of January, numerous his backers stormed and vandalised government buildings in the capital, the capital city.
The police stepped in and around fifteen hundred individuals were arrested.
The magistrates found that the demonstrators had been provoked by him whose strategy, they said, was for the national armed forces to intervene, restore order and bring him back to power.
At the time, the legal team called the decades-long sentence extremely harsh.
He was also prohibited from running for public office until 2060 - eight years after the completion of his term.
The ex-leader called the trial a "witch hunt and said it was designed to prevent him participating in the 2026 national vote.