Church administrators were appointed to run all three diocese.
But days after returning to Rome, a chastened pope, citing new information, sent sexual abuse investigator Archbishop Charles Scicluna of Malta to Chile to speak to victims, witnesses and other church members.
Pope Francis remains in the spotlight, following recent comments about climate change with pleads to oil executives that call for clean fuel.
The pope accepted Barros' resignation despite previous attempts to defend the bishop. But so far, the pope has accepted only three resignations. He met survivors at the Vatican and has been strong in his criticism of how the Chilean bishops handled the situation.
The pontiff has promised Catholics in Chile that the church would "never again" ignore them or participate in covering up cases of abuse in their country.
The two investigators will meet Wednesday with Canon law experts from Chilean dioceses who will provide "technical and legal assistance" in order to "provide adequate responses to each case of child sexual abuse committed by clerics or religious", Scicluna told reporters.
Barros was a protégé of the Rev. Fernando Karadima, who in 2011 was found guilty by the Vatican and ordered to retire for abusing dozens of minors over a decades-long period, with some allegations dating back to the 1980s.
However, after having read a 2,300-page report on abuses in Chile, the pope admitted having made "grave mistakes" and apologized to victims.
A Vatican official said yesterday's move represented a first step towards re-ordering the battered Roman Catholic Church in Chile and that the pope was still considering the positions of the other prelates.
The announcement came in a June 11 communique from the Vatican, along with the resignation of two other Chilean bishops.
The Catholic Church's upcoming big family rally in Ireland will feature workshops on hot-button issues facing Catholic families, including priestly sexual abuse, weathering divorce and ministering to lesbian and gay faithful.
Claros said Barros' exit was the "minimum condition" to begin a dialogue with the Vatican to try to rebuild peace in the diocese, and he called for a process to find "truth, justice and reparation" for the damage caused.