Earlier in the day, security forces had taken up position in front of her office, blocking Ortega from entering the building.
On Friday, the OAS' Inter-American Commission on Human Rights ordered Venezuela to protect Ortega, saying her life was at risk after she launched an investigation into the legality of the new, all-powerful Constituent Assembly.
Chief prosecutor Luisa Ortega had asked a local court to halt the inauguration. "I denounce this arbitrary act before the national and worldwide community".
He said he does not want to give Mr Maduro any added ammunition to blame the "Yankees" for the oil-rich nation's economic and political crisis.
In recent years, a number of high profile opposition leaders indicted for their role in attempting to overthrow the elected government have fled the country.
Former Foreign Minister Delcy Rodriguez, a hard-line Maduro loyalist, was named president of the new assembly.
Her opening speech attacked the opposition as "fascist" and warned the global community against interfering.
The body's 545 delegates were expected to be installed at the legislative palace in a room just metres from the chamber where the opposition-controlled National Assembly meets.
Meanwhile, the South American trade bloc Mercosur has chose to suspend Venezuela for failing to follow democratic norms.
At least 40 global leaders had called on Maduro not to launch the new assembly, saying they would not recognize it.
The former foreign minister also lashed out at US President Donald Trump, whose government established a series of sanctions against Venezuelan officials as a form of pressure to stop the installation of the Constituent Assembly.
Venezuela's controversial "Constituent Assembly", a new legislative body with supreme powers packed with supporters of President Nicolas Maduro, began its first session in Caracas on Friday.
Opposition lawmakers have pledged to remain in power no matter what action is taken by the constitutional assembly, raising the possibility of two governing bodies operating side by side, with neither recognizing the other.
The new constituent assembly, which Ortega said was fraudulently elected last weekend, unanimously chose to remove her in its first session on Saturday.
Maduro on Wednesday rejected accusations that his government inflated turnout figures, branding them part of an effort to stain what he called a clean and transparent vote.
The Vatican is urging Venezuela's government to "avoid or suspend" the new assembly tasked with rewriting the constitution while holding near-absolute powers.
It was not immediately evident whether Lopez would also be returned from jail to house arrest.
On Monday, the Trump administration sanctioned Maduro and froze any assets he might have under US jurisdiction.
Venezuela's government perceives the commission to be under U.S. influence and brushes off its pronouncements.