A Vatican statement on Saturday said the pope had named Bishop Celestino Aós Braco of the Chilean city of Copiapó, as "apostolic administrator" to run the Santiago archdiocese until a new archbishop is named to succeed Ezzati, Reuters reported.
Ezzati, 77, faces multiple charges of cover up, including some relating to the case of Oscar Munoz, a former top aide to the Santiago Archbishopric, who is facing trial on charges he abused and raped at least five children. He denies wrongdoing.
In October, he exercised his right to silence after being summoned for questioning by a state prosecutor over the allegations.
His resignation brought to eight the number of bishops who have stepped down since all of the country’s 34 bishops offered their resignations en masse during an emergency meeting with the pope last May over allegations of a cover-up.
That meeting was held after Vatican investigators produced a 2,300-page report alleging that senior Church officials in Chile had failed to act on abuse claims and in some cases hid them.
The decision to accept Ezzati's resignation comes at time of growing criticism over the Church's response to a decades-long sexual abuse crisis that has gravely damaged its standing around the globe.
Victims of sexual abuse by clergymen say a top-level conference at the Vatican last month failed to come up with concrete measures to tackle the issue.
An Australian court last week sentenced former Vatican treasurer Cardinal George Pell to six years in prison for sexually abusing two choir boys in Melbourne - the most senior Catholic to be convicted for child sex offenses.