Bolsonaro has been taken into custody after authorities concluded he posed a definite escape threat while under house arrest.
The former head of state was convicted of planning a military coup in last fall and given more than a 27-year term in incarceration, but he continued under home detention pending court reviews.
Brazilian Supreme Court Justice Alexandre de Moraes said the action to imprison the elderly politician was a precautionary step after "new facts" were revealed.
This encompassed trying to remove his tracking device and a summons to a demonstration that could enable a possible escape.
In a paperwork permitting the detention, Justice Moraes said information from the facility tracking his home detention suggested the ex-president's "intention to break the electronic ankle bracelet to ensure success in his flight.
This, it said, would be "facilitated by the disorder caused by the protest called by his offspring.
His offspring, his son Flávio, who holds office as a senator, called for a assembly of his followers near the former president's residence to take place on Saturday night.
Flávio Bolsonaro wrote on digital networks on last Friday: Do you plan to struggle for your nation, or observe everything from your mobile device there on your settee? I urge you to struggle with us."
He said the demonstration would be so followers could seek divine intervention for his physical condition and for the reestablishment of democratic governance in our land."
Part of the magistrate's decision was the potential of his move to embassies near the dwelling, considering that the investigations revealed a history of planning to seek refuge through a consular facility", a declaration said.
The court filing emphasizes that the US embassy in the capital, Brasilia, is located around 13km from Bolsonaro's home.
His judicial problems have drawn the ire of fellow populist conservative United States President Trump, prompting him to impose a half-rate duty on Brazilian product imports.
Bolsonaro is being detained in a federal law enforcement building in the capital and will experience a detention review on the next day.
It was only on the previous day that the former president's lawyers asked the Supreme Court to permit him to complete his entire prison term under house arrest, with tracking devices.
They also asked that the former president be authorized to exit his dwelling for medical care, saying he demanded ongoing care for pulmonary infections and other illnesses.
The former president was found guilty of heading a plot aimed at maintaining his control after he failed to win the 2022 election to his ideological adversary, Luiz Inácio Lula da Silva.
High Court judges said that he had knowledge of a plan which included plans to kill Lula and his running partner, his vice-presidential candidate, and to detain and kill Justice Moraes - the Supreme Court justice who has been presiding over the former president's case.
The conspiracy was thwarted because it didn't receive the support of the military leaders. Lula was inaugurated without issue on the first day of 2023.
But a following week, on 8 January, numerous his backers invaded and destroyed government buildings in the national capital, Brasília.
The law enforcement intervened and around 1,500 people were arrested.
The judges found that the demonstrators had been incited by him whose scheme, they said, was for the national armed forces to intervene, bring back stability and reinstate his authority.
At the moment, the legal team called the over 27-year sentence unreasonably severe".
He was also prohibited from campaigning for office until twenty-sixty - a decade minus two years after the conclusion of his imprisonment.
The ex-leader called the court case a political persecution and said it was aimed at blocking him competing in the 2026 national vote.