In a letter given to them at the end of their 3-day Vatican summit, the Holy Father thanked them for their "frank" dialogue in Rome.
Four of Chile's bishops have resigned in connection with the child sex abuse scandal engulfing the country's Catholic church as the emergency Vatican session overseen by Pope Francis comes to a close.
The Chilean bishops said the contents of the document were "absolutely deplorable" and showed an "unacceptable abuse of power and conscience", as well as sexual abuse.
"In communion with (the Pope) we want to re-establish justice and contribute to repairing the damage caused", they wrote.
On Thursday evening, Francis promised "changes" to the Chilean church to "restore justice" following the private meetings with the delegation.
Francis reiterated his heartfelt apology to the bishops and the victims, saying he is close to them and is united with them in "one single will and with the firm intention to fix the damages done".
A Vatican spokesman said he could not confirm a report by Argentina's Clarin newspaper that Barros and several other bishops had offered the pope their resignations.
The BBC reported that the bishops were handed a 10-page document during the Vatican talks by Pope Francis, which accused the Church in Chile's hierarchy of negligence in cases of sexual abuse, and that the bishops said that if the Pope chose not to accept their resignations, they would "continue doing our pastoral work".More news: Russia-Germany gas pipeline raises intelligence concerns
Francis said last month he would take short-, medium- and long-term measures to try to fix the damage to the Chilean church's credibility.
After receiving the Scicluna-Bertomeu report, though, Francis did a volte-face, blaming a "lack of truthful and balanced information" about the case for his missteps, and invited the three main whistleblowers to the Vatican so he could apologize in person.
In 2011, Karadima was convicted by the Congregation for the Doctrine of Faith of abusing minors and sentenced to a life of prayer and solitude.
On Thursday three other bishops offered their resignations ahead of Friday's statement from all the bishops.
The letter ended with a call for the bishops to create a church which listens to "the hungry, the imprisoned, the migrant and the abused". Francis further enraged Chileans and drew sharp rebuke from his top abuse adviser when, during a January trip to Chile, he said the accusations against Barros were "calumny" and said he was "certain" he was innocent.
Picture: Bishop Juan Ignacio Gonzalez Errazuriz of San Bernardo, Chile, and Auxiliary Bishop Fernando Ramos Perez of Santiago, Chile, arrive for a press conference in Rome on 18th May.
Naturally the Pope will have decisions to make and there will be resolutions, but those will come later, the bishop said, adding that the time they had was one of discernment and returning to their heart of their mission, which is Christ.