The new constituent assembly, which Ms Ortega said was fraudulently elected last weekend, unanimously chose to remove her in its first session on Saturday.
"We will solve our differences among Venezuelans without any imperial mandate", she said to delegates and supporters gathered at the Legislative Palace. "The violent fascists, those who wage economic war on the people, those who wage psychological war: Justice is coming for you!".
The Vatican statement called for the "avoidance or suspension of ongoing initiatives such as the new constitutional assembly that, more than favoring reconciliation and peace, promote a climate of tension and confrontation and mortgage the future".
Opposition leaders are calling for a march to the center of Caracas on Friday to protest the creation of the 545-member constituent assembly.
Rodriguez promised quick action against the government's opponents.
Brazil will propose suspending Venezuela from the sub-regional Mercosur trade bloc until the restoration of democracy in the country, Brazilian Foreign Minister Aloysio Nunes said Friday.
Venezuela was previously suspended in December for failing to uphold commitments it made when it joined the group in 2012. It says the constituent assembly is a way for the president to cling to power.
It will have sweeping powers to upend institutions and in theory could even remove Maduro, a fact held up by government supporters as a sign of its independence from the government.
The president of Venezuela's Constituent Assembly Delcy Rodriguez, front and center, leads the newly sworn-in members as they pose for a photo Friday..
Protests against the inauguration of the assembly by the opposition were relatively modest.
As members of the contested assembly unanimously voted to ax the attorney general, pro-government demonstrators chanted slogans against her. Ortega launched a criminal investigation into the elections authority Wednesday after Smartmatic, the company that provides the country with its voting machines and software, said it couldn't stand by results that had been inflated by at least 1 million of a purported almost 8.1 million votes. Opposition sources dispute the figure, saying fewer than four million people voted.
The constituent assembly replaced Ortega with human rights ombudsman Tarek Saab, a government ally whom the opposition says has turned a blind eye to state abuses.
The commission urged the Venezuelan government to do whatever necessary "to guarantee the life and physical integrity" of its chief prosecutor.
On Tuesday, opposition leaders Leopoldo López and Antonio Ledezma, who had been under house arrest, were taken to a military prison.
A prominent Venezuelan opposition leader has been returned to his home after spending several days jailed. Since Sunday's election, it has shed almost 83 percent against the dollar on the black market, doubling the cost of bread and tomatoes in less than a week. "The dead are too many and I do not think there are other criteria to follow that is not in the common good of the people", he insisted. But now it's 18,000!
Venezuela's socialist government is widely blamed for the crisis. She said she did not know how many of her employees remained in the building.