In an unprecedented move, all Chile's 34 bishops offered to resign en masse last month after attending a crisis meeting with the pope over allegations of a cover-up of sexual abuse in the South American nation.
It was not immediately clear if Monday's move meant the pope would not accept any of the other resignations.
Besides Barros, the pope also agreed to the departures of Cristian Caro Cordero, bishop of Puerto Montt, and Gonzalo Duarte Garcia de Cortazar, bishop of Valparaiso.
Church administrators were appointed to run all three diocese.
Pope Francis has promised Chilean Catholics scarred by a culture of clergy sexual abuse that "never again" would the Church ignore them or the cover-up of abuse in their country.
Victims accused Barros of having witnessed the abuse but doing nothing to stop it. Barros has denied the allegations.
The Vatican's most experienced sexual abuse investigator, Archbishop Charles Scicluna visited Chile earlier this year to look into the scandal. He has been sent back to Chile to gather more information.
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