Bolsonaro has been detained after authorities found he posed a definite escape threat while under home confinement.
The ex-president was convicted of planning a government overthrow in the ninth month and given more than over two decades in incarceration, but he was staying under home detention pending legal challenges.
High Court Judge the presiding justice said the action to imprison the 70-year-old politician was a precautionary step after recent developments came to light.
This encompassed seeking to disable his tracking device and a summons to a supporters' gathering that could facilitate a possible escape.
In a document approving the arrest, Justice Moraes said data from the facility tracking Bolsonaro's house arrest suggested the ex-president's plan to remove the tracking monitor to guarantee victory in his escape.
This, it said, would be made easier by the chaos caused by the demonstration called by his offspring.
His offspring, his son Flávio, who holds office as a senator, called for a meeting of his backers near the former president's residence to take place on Saturday evening.
The senator wrote on online platforms on last Friday: Do you plan to struggle for your homeland, or see it all from your phone there on your couch? I urge you to struggle with us."
He said the vigil would be so backers could seek divine intervention for his well-being and for the return of democracy in our nation."
Part of the magistrate's decision was the potential of the former president's transfer to foreign missions near the dwelling, considering that the inquiries revealed a history of planning to request asylum through a embassy office", a declaration said.
The court filing highlights that the United States embassy in the national capital, Brasilia, is located around approximately 13 kilometers from the former president's residence.
The former president's legal troubles have generated frustration from fellow right-wing populist United States President Donald Trump, leading him to implement a 50% tariff on goods coming from Brazil.
The former president is being detained in a national police facility in Brasilia and will experience a imprisonment assessment on the next day.
It was only on Friday that the ex-leader's attorneys asked the High Court to allow him to complete his entire prison term under house arrest, with tracking devices.
They also asked that Bolsonaro be permitted to leave his home for medical care, saying he demanded regular treatment for pulmonary infections and other ailments.
The former president was found guilty of orchestrating a plot aimed at keeping him in power after he lost the 2022 election to his political opponent, Lula.
Top judicial officials said that he knew of a scheme which encompassed plans to murder his opponent and his running partner, his vice-presidential candidate, and to arrest and execute Alexandre de Moraes - the Supreme Court justice who has been managing his judicial proceedings.
The plot was prevented because it couldn't obtain the endorsement of the military leaders. Lula was inaugurated without problem on 1 January 2023.
But a seven days after, on the eighth of January, thousands of Bolsonaro supporters stormed and vandalised public facilities in the capital, the capital city.
The police took action and around 1,500 people were taken into custody.
The judges found that the rioters had been provoked by the former president whose plan, they said, was for the Brazilian military to step in, restore order and reinstate his authority.
At the moment, his attorneys called the 27 years and three months sentence unreasonably severe".
He was also banned from campaigning for office until the year 2060 - eight years later after the completion of his term.
The former president called the trial a "witch hunt and said it was designed to prevent him participating in the next presidential race.
Lena is a professional organizer and minimalist lifestyle coach with over a decade of experience helping people simplify their homes.