The entire Chilean delegation of bishops tendered its resignation to the Pope last month after a series of meetings at the Vatican.
The announcement came in a June 11 communique from the Vatican, along with the resignation of two other Chilean bishops.
Besides Barros, the pope also agreed to the departures of Cristián Caro Cordero, bishop of Puerto Montt, and Gonzalo Duarte García de Cortázar, bishop of Valparaiso.
Taking over as in Barros' stead is Bishop Jorge Enrique Conchua Cayuqueo, O.F.M., auxiliary bishop of Santiago, who will serve as apostolic administrator for the Diocese of Osorno.
One of the victims, Juan Carlos Cruz, told Chilean radio that by accepting the resignations, Pope Francis had "sent a message to the world that this culture of abuse and cover-up won't be tolerated any longer". Victims accused Bishop Juan Barros of having witnessed the abuse but doing nothing to stop it. Barros has denied the allegations.
The scandal revolves around priest Fernando Karadima who molested several boys in Chile's capital of Santiago in the 1970s and 1980s.
They questioned Barros' suitability to lead given he had been a top lieutenant of Chile's most notorious predator priest and had been accused by victims of witnessing and ignoring their abuse by that priest.
New abuse accusations have emerged in recent weeks against the Church in Chile, including allegations against the pope's own Jesuit order.
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The Vatican's most experienced sexual-abuse investigator, Archbishop Charles Scicluna, visited Chile this year to look into the scandal.
His later comments in apparent support of Barros set in motion a series of events that resulted in the pope's decision Monday to accept the three resignations.
All of Chile's 34 Roman Catholic bishops had offered their resignations. However, the pope, who hails from Argentina, initially defended the prelate in January, saying the allegations were "slander".
Karadima, who is now 87 and living in a nursing home in Chile, has always denied all charges against him.
It is not yet known how many, if any, more of Chile's bishops will depart from office.
The Church said it would name a delegate next Monday to be stationed in Santiago and receive accusations of abuse, part of a new effort to help victims seek quick justice on still-open cases, some of which go back decades.
Francis realized he had misjudged the Chilean situation after meeting with Cruz and reading a 2,300-page report compiled by two leading Vatican investigators about the depth of Chile's scandal.
Since 2000, about 80 Catholic priests have been reported to authorities in Chile for alleged sexual abuse.
Joining him is Marie Collins, an Irish survivor of abuse who resigned from O'Malley's panel a year ago in frustration over the Vatican's resistance to listening to victims.