Bolivian opposition senator Jeanine Annes declared himself interim president of the South American country after the resignation of Evo Morales.
Lawmakers from Mr Morales's party boycotted the session, meaning there was no quorum for the appointment.
But Ms Áñez stated that she was the next in the constitution and promised to hold elections soon.
Mr Morales condemned this message, describing Ms Annes as a "senator of the right-wing coup".
The former president fled to Mexico, saying he sought asylum there because his life was in danger.
He resigned Sunday after weeks of protests over a contested result of the presidential election. He said he was forced to retire but did so willingly "so that there would be no more bloodshed."
How did the senator become interim president?
Ms. Annes took temporary control of the Senate on Tuesday, putting her on the next line for the presidency.
The former Senate Deputy Leader took the position after a series of resignations.
The parliamentary session for her appointment was boycotted by MPs from the left-wing Mr Morales Socialist Movement, who said it was illegitimate.
"Prior to the final absence of the President and Vice-President … as chairman of the House of Senators, I immediately assume the presidency as provided for in the constitutional order," said Ms Annes, applauding opposition members.
Bolivia's highest constitutional court upheld the assumption of power.
Taking to Twitter from Mexico, Mr. Morales condemned "the craziest, most insidious coup in history."
How did we get here?
Mr Morales, a former coca farmer, was first elected before 2006, the first indigenous leader in the country.
He won calls to fight poverty and improve Bolivia's economy, but sparked controversy by rejecting constitutional boundaries to run for a fourth term in the October elections.
The pressure on him increased after his narrow victory in the vote last month.
The result was called into question by the United States Organization, a regional body that found "clear manipulation" and called for the result to be canceled.
In response, Mr. Morales agreed to hold new elections. But his main rival Carlos Mesa ̵
The Chief of Armed Forces, Gen. Williams Kaliman, urged Mr. Morales to step down in the interests of peace and stability.
Announcing his resignation, Mr Morales said that he had taken the decision to stop fellow socialist leaders from being "harassed, persecuted and threatened".
He escapes to Mexico after unrest in the streets of Bolivian capital La Paz supporters of the socialist leader clashing with security forces.
After arriving in Mexico City on Tuesday, he thanked Mexican President Andres Manuel Lopez Obrador, whom he credits for saving his life.
"As long as I have a life, I will stay in politics, the struggle continues. All people in the world have the right to be free from discrimination and humiliation," he said.