The Vatican said that Francis has written to Chilean Cardinal Javier Errazuriz and Australian Cardinal George Pell thanking them for their five years of service on the so-called Group of Nine, or C-9.
Francis also bid farewell to Congolese Cardinal Laurent Monsengwo Pasinya, who has not been implicated in the scandal but, age 79, recently retired as archbishop of Kinshasa.
Mr Errazuriz, 85, has been accused by Chilean abuse survivors of having covered up for predator priests while he was archbishop of Santiago, a charge he has denied.
Mr Pell, 77, took leave from his job as the Vatican's economy minister to stand trial in his native Australia on historic charges of sex abuse, which he denies.
Their continued presence on the C-9 had been a source of scandal for Francis, given the explosion of the abuse and cover-up crisis this year.
Francis himself was implicated in the scandal after he strongly defended a Chilean bishop accused of covering up for the country's most notorious predator priest - a position he took apparently on the advice of Mr Errazuriz.
After Francis realised his errors and apologised, he summoned the presidents of all the world's bishops conferences to Rome for a three-day meeting in February to discuss protecting young people from paedophiles. That summit has taken on enormous weight given the eruption of the scandal in the US.
The Vatican made no mention of the accusations against Mr Errazuriz and Mr Pell in explaining their departures, and said for now they would not be replaced.
Francis appointed the C-9 in 2013 to help him reform the Vatican and reorganise its bureaucracy. That work is wrapping up, with the finalising of a new document outlining the work and mission of the various congregations that make up the universal government of the 1.2 billion-strong church.
A statement from the Vatican press office noted that the cabinet members asked Francis in September to reflect on the future composition, structure and work of the C-9, taking into consideration especially the advanced ages of some of its members.
Mr Errazuriz, who retired as Santiago archbishop in 2010, had announced publicly in November that he had removed himself from the group. He is currently the subject of civil litigation in Chile by victims accusing him of covering up for recently defrocked priest Fernando Karadima.
Though he has been away from Rome since announcing his leave of absence in June 2017, Mr Pell technically remains prefect of the Vatican's economy secretariat.
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