Bolsonaro has been arrested after authorities concluded he posed a concrete flight risk while under home confinement.
The former head of state was sentenced of orchestrating a military coup in last fall and given more than a 27-year term in incarceration, but he remained under home detention pending appeals.
Brazilian Supreme Court Justice Justice Moraes said the move to detain the septuagenarian politician was a precautionary step after recent developments emerged.
This included attempting to break his electronic bracelet and a invitation to a demonstration that could "allow for a chance to flee".
In a document approving the detention, the judge said intelligence from the centre monitoring the former president's confinement suggested the former leader's plan to remove the surveillance device to ensure success in his getaway".
This, it said, would be assisted by the chaos caused by the protest called by his child.
His offspring, Flávio, who serves as a congressional representative, called for a gathering of his backers near his father's house to take place on Saturday night.
The senator wrote on online platforms on Friday: "Are you going to fight for your country, or watch it all from your mobile device there on your sofa? I invite you to fight with us."
He said the vigil would be so backers could "pray for his physical condition and for the return of democracy in our land."
Part of the magistrate's decision was the chance of Bolsonaro's "relocation to diplomatic missions near the residence, considering that the investigations revealed a record of planning to seek refuge through a consular facility", a declaration said.
The legal document emphasizes that the US embassy in the capital, Brasilia, is situated around 8 miles from his dwelling.
Bolsonaro's legal woes have drawn the ire of fellow right-wing populist US President Trump, causing him to implement a half-rate duty on imports of Brazilian goods.
He is being kept in a federal law enforcement building in the capital and will undergo a imprisonment assessment on Sunday.
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 electronic monitoring.
They also requested that he be permitted to depart his residence for healthcare, saying he needed regular treatment for pulmonary infections and other illnesses.
The former president was convicted of orchestrating a conspiracy aimed at maintaining his control after he was defeated in the 2022 election to his political opponent, Lula.
Supreme Court justices said that he knew of a plot which included plans to assassinate the current president and his VP candidate, Geraldo Alckmin, and to detain and kill Alexandre de Moraes - the High Court judge who has been managing Bolsonaro's trial.
The conspiracy was stopped because it couldn't obtain the backing of the military leaders. His successor was sworn in without incident on January 1st, 2023.
But a following week, on the eighth of January, thousands of his followers invaded and destroyed government buildings in the capital, Brazil's capital.
The police stepped in and around 1,500 people were detained.
The judges found that the protesters had been encouraged by the former president whose scheme, they said, was for the Brazilian military to intervene, bring back stability and bring him back to power.
At the period, the legal team called the 27 years and three months sentence extremely harsh.
He was also barred from campaigning for office until twenty-sixty - eight years after the conclusion of his imprisonment.
The former president called the court case a political persecution and said it was designed to prevent him competing in the 2026 presidential election.
Elena Marchetti is a technology journalist with a passion for demystifying complex topics. She has been covering tech trends for over a decade.