All of Chile's 34 Roman Catholic bishops resigned last month following a meeting in Rome during which Francis said the bishops were all collectively responsible for covering up clerical sexual abuse in their dioceses.
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.
The sex abuse scandal is among the most challenging issues facing Francis, who has said he felt "pain and shame" about the church's failure for decades to confront cases of abuse by priests that have come from across the globe.
Karadima's victims accused Juan Barros of knowing about the abuse but saying and doing nothing about it.
The third exiting priest, Bishop Cristian Caro of Puerto Montt, stands accused by some Catholics of having misinformed Francis on the allegations against Barros.
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The resignation of Bishop Barros comes after years of accusations and questions concerning his knowledge of abuse by his mentor and protests when Pope Francis appointed the then-head of the military ordinariate to head the Diocese of Osorno in 2015.
By accepting Barros' resignation, Francis essentially gave Scicluna and Bertomeu a hand in helping to heal the divisions in a diocese where Barros never was fully accepted as bishop.
"Today begins a new day for the Catholic Church in Chile and hopefully the world", Juan Carlos Cruz, the key witness in the abuse case, wrote on Twitter.
Opponents have been vocal about their opposition to Barros ever since, with some of the most outspoken being victims of Karadima, who in 2011 was found guilty by the Congregation for the Doctrine of the Faith of sexually abusing several minors during the 1980s and 1990s, and sentenced to a life of prayer and solitude.
The Pope's move comes after he received two groups of victims of Fernando Karadima at the Vatican.
The Vatican said the pope had also accepted the resignation of two other bishops in Chile - Msgr.
Francis has apologised to the victims and admitted he had made "grave mistakes" after reading a 2,300-page report on abuses in Chile.
During his weeklong trip through Chile and Peru in January, Francis opened with a somber apology for sexual abuse by priests. Francis said he had misjudged Juan Barros and the events in Chile because he hadn't been given "truthful and balanced information".