During his visit to Chile in January, Francis upset abuse survivors and their loved ones when he dismissed the allegations against Barros as "calumny", claiming there was no evidence and saying he had never seen proof against the bishop.
Barros submitted his resignation to Pope Francis alongside every other active bishop in Chile at the close of a May 15-17 meeting between the pope and Chilean prelates, during which Francis chastised the bishops for systematic cover-up of abuse throughout the country.
Church administrators were appointed to run all three dioceses.
Maltese archbishop Charles Scicluna and fellow papal envoy Jordi Bertomeu will take witness statements from victims of sexual abuse within the Church and provide instruction to Chilean dioceses to respond adequately to any new complaints.
In addition to Barros, the others who resigned are Bishop Gonzalo Duarte of Valparaiso and Bishop Cristian Caro of Puerto Montt.
Pope Francis' appointment of Barros to Osorno in 2015 was met with a wave of objections and calls for his resignation.
Pope Francis has, according to BBC, apologized to victims after more than 1,000 Chileans wrote to him, asking him to reconsider the installation of Juan Barros as bishop of the Chilean city of Osorno.
"The band of delinquent bishops ... begins to disintegrate today".
Paul’s Skyscraper-Scaling Raccoon Captivates Internet
Minnesota Public Radio branded the raccoon #mprraccoon , a hashtag that spread around the world. Paul Animal Control believed it may have been there all night before it started heading skyward.
Griezmann: Today isn't the day to discuss my future
Monaco have already sold Fabinho to Liverpool this month, and they are set to make further profit with the sale of Lemar. A statement on Atletico's website confirmed the clubs will work over the next few days to complete the transfer.
UK Labour MPs Worried by Govt's EEA Deal With EU - Frontbencher
He also warned any attempt by so-called hard Brexiteers to "overthrow" Mrs May would be "completely mad". Government sources signalled to the Press Association that ministers were set to back the move.
After Francis returned to the Vatican, he sent the Roman Catholic Church's top sex crimes expert to Chile to investigate further.
The Vatican in 2011 sentenced Karadima, a powerful preacher close to Chile's elite, to a lifetime of penance and prayer for his sex crimes.
Pope Francis has accepted the resignation of a Chilean bishop he robustly defended earlier this year despite claims of a cover-up of clerical sexual abuse, a move that later forced the pontiff into making a public apology.
Several members of the Chile's Catholic Church hierarchy are accused by victims of ignoring and covering up child abuse by Chilean paedophile priest Fernando Karadima during the 1980s and 1990s. "Three corrupt bishops are out", said Juan Carlos Cruz, one of Karadima's victims who was received by the pope in May along with two other men the priest had abused.
Barros, who is a central figure in the controversy, has been accused of covering up abuse committed by another priest in the 80s and 90s.
Juan Carlos Claret, spokesman for a group of lay Catholics in Osorno who fought for Barros' removal from office, said it was a "minimum condition" that they had sought from the pope.
"The resignation of these bishops should not dilute their criminal responsibility", he said.
Since 2000, about 80 Catholic priests have been reported to authorities in Chile for alleged sexual abuse.