In an unprecedented move, all Chile's 34 bishops offered to resign last month after attending a crisis meeting with Francis over allegations that sexual abuse in the country's Catholic church had been covered up.
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. He thanked the pope for his concern for the common good and said he prayed "that one day all the truth will shine".
The Vatican's most experienced sexual abuse investigator, Archbishop Charles Scicluna visited Chile earlier this year to look into the scandal.
Karadima's victims have long accused Barros of knowing about the abuse but saying and doing nothing about it. Barros has repeatedly denied playing any role.
The two other bishops, who had reached the customary retirement age of 75, were Archbishop Cristian Caro Cordero of Puerto Montt and Bishop Gonzalo Duarte Garcia de Cortazar of Valparaiso.
Three Chilean Bishops have presented their resignations letters to Pope Francis over allegation of sexual misconduct.
The decision of whether to accept the bishops' resignations is up to Pope Francis.
"It's a new day for the Catholic Church of Chile!"
After Francis returned to the Vatican, he sent the Roman Catholic Church's top sex crimes expert to Chile to investigate further.
But by also accepting the resignations of the two other bishops, Francis is making clear that the troubles in Chile's church do not rest on Barros' shoulders alone, or on those of the more than 40 other priests and three other bishops trained by the Rev. Fernando Karadima.
He later apologised to victims, following criticism from Cardinal Sean O'Malley, a Vatican pointman on clerical sex abuse.
An worldwide family rally the Catholic Church is hosting in Ireland will feature workshops on hot-button issues facing Catholic families, including protecting children from clergy sexual abuse, weathering divorce and ministering to lesbian and gay faithful.
They accused Bishop Barros of using his position in the Church to cover up the actions of his mentor, Fr Fernando Karadima, who was found guilty by the Vatican of sexually abusing children.
Francis apologized to the victims and admitted he had made "grave mistakes" after reading a 2,300-page report on abuses in Chile.
Since 2000, about 80 Catholic priests have been reported to authorities in Chile for alleged sexual abuse.
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.