Bolsonaro has been detained after authorities concluded he posed a definite escape threat while under house arrest.
The former head of state was convicted of plotting a government overthrow in September and sentenced more than a 27-year term in jail, but he was staying under house arrest pending legal challenges.
Brazilian Supreme Court Justice Justice Moraes said the move to detain the elderly politician was a safety action after "new facts" were revealed.
This involved attempting to break his ankle monitor and a call for a public vigil that could enable a potential flight.
In a paperwork permitting the arrest, the magistrate said data from the facility tracking the former president's confinement suggested the ex-president's aim to disable the surveillance device to secure accomplishment in his getaway".
This, it said, would be made easier by the confusion caused by the protest called by his son.
His son, Flávio Bolsonaro, who holds office as a legislator, called for a gathering of his supporters near his father's house to take place on Saturday night.
His son wrote on online platforms on last Friday: Do you plan to struggle for your country, or see it all from your smartphone there on your sofa? I urge you to battle with us."
He said the demonstration would be so followers could seek divine intervention for his well-being and for the restoration of democratic rule in our land."
Part of the magistrate's determination was the possibility of the former president's transfer to diplomatic missions near the home, considering that the inquiries revealed a background of planning to seek refuge through a diplomatic representation", a announcement said.
The legal document underscores that the American diplomatic mission in the capital, Brasilia, is located around 13km from his dwelling.
Bolsonaro's legal woes have generated frustration from fellow conservative nationalist US President President Trump, prompting him to implement a 50% tariff on imports of Brazilian goods.
Bolsonaro is being kept in a national police facility in Brasilia and will experience a detention review on the next day.
It was only on the previous day that the his legal team asked the Top Court to permit him to complete his entire prison term under house arrest, with digital surveillance.
They also asked that Bolsonaro be allowed to depart his residence for medical treatment, saying he required regular treatment for lung conditions and other health problems.
The former president was convicted of heading a plot aimed at retaining his authority after he failed to win the presidential race to his political opponent, President Lula.
Top judicial officials said that he knew of a scheme which included plans to murder the current president and his VP candidate, Alckmin, and to arrest and execute the presiding judge - the top judicial official who has been presiding over the former president's case.
The plot was prevented because it couldn't obtain the endorsement of the army and air force commanders. His successor was took office without problem on the first day of 2023.
But a week later, on the eighth of January, many Bolsonaro supporters stormed and vandalised official structures in the federal district, Brasília.
The security forces took action and around fifteen hundred individuals were detained.
The judges 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, the legal team called the decades-long sentence unreasonably severe".
He was also banned from seeking elected position until 2060 - eight years later after the end of his sentence.
The former president called the legal proceedings a political persecution and said it was aimed at blocking him running in the next presidential race.
Elara Vance is a tech journalist and business analyst with over a decade of experience covering digital transformation and startup ecosystems.