Auxlilary bishop in Brisbane Brian Finnigan was accused of trying to protect himself and the church when he gave evidence earlier this month. There were calls for him to be sacked.
Aged 77, Bishop Finnigan offered his resignation two years ago as Canon Law requires of Catholic clergy. The Pope accepted it at the end of December, on the grounds of his age.
In a letter sent to clergy he said: "I am grateful that it has now come to pass. At 77 years of age, energy levels and mental agility have diminished. From those whom I may have disappointed, I seek forgiveness."
The bishop, who was secretary to the Bishop of Ballarat over a period when Ballarat priest Gerald Ridsdale was abusing boys, had told the commission publicly that he only found out about about the abuse when the priest was charged in 1993. However, the commission heard privately that he had known about the complaints at least 12 years earlier.
Bishop Finnigan was the youngest of 12 children and was ordained priest in 1970 and bishop in 2002.
He said: "It has been a great privilege to serve in the Archdiocese of Brisbane, and I am now looking forward to the next phase of my life. All those with whom I have worked and whom I have served can be assured of my prayerful support in the coming years."