Cardinal Sean Brady, the leader of the Catholic Church in Ireland, has apologised and asked for forgiveness as his retirement was confirmed by the Vatican.
The cleric, whose final years at the head of the clergy were dogged by abuse scandals, handed in his resignation on age grounds last month after turning 75, as required under canon law.
Archbishop Eamon Martin will take over as Archbishop of Armagh and Primate of All Ireland -- the 116th man to fill the role.
The case is the latest to hit the Catholic Church.
Cardinal Keith O'Brien, Archbishop of St Andrews and Edinburgh, resigned in 2013 after admitting decades of sexual behaviour with other clerics and was exiled from Scotland by the Vatican.
Cardinal Brady has faced repeated calls from clerical sex abuse survivors to quit over his involvement in the Brendan Smyth case.
The teacher and canon lawyer attended meetings during which two victims of the notorious paedophile priest were sworn to secrecy during an internal church inquiry in 1975 into the abuse of two children.Their evidence was never handed over to police, allowing Smyth to continue abusing other youngsters countless times before he was finally jailed in 1994.
The Cardinal insisted his role in the inquiry was as a notetaker.
In a farewell message at mass in St Patrick's Cathedral in Armagh the church leader said he recalled Pope Francis' motto "miserando atque eligendo" which he said "challenges and inspires me with its message of God having mercy and at the same time choosing us, despite our sinfulness".
"It reminds me that I too need to say sorry and to ask forgiveness. And I do so again, now," Cardinal Brady said.
Last month Pope Francis promised to hold bishops to account for the protection of children and begged forgiveness from victims after he celebrated a Mass with six survivors at the Vatican.
One of them, Irish woman Marie Kane, said she asked the pontiff to remove Cardinal Brady from his post because of the way he handled abuse allegations.
The acceptance of a bishop's resignation within one month is unusual for the Catholic Church but the departure has been flagged for some considerable time.
Cardinal Brady led the church in Ireland for more than 17 years during which time investigations exposed shocking levels of abuse.
His successor, Archbishop Martin, is a 52-year-old Derry-born former teacher who was named as Coadjutor Archbishop of Armagh early in 2013.
Last December an investigation by church watchdog the National Board for Safeguarding Children said Cardinal Brady made a "commendable decision to gather and document whatever information was available" about abuse allegations in his own archdiocese on taking up his role as Primate of All Ireland in 1996.
At the time he said he was sorry for the suffering of victims. He has also apologised to Smyth's victims, although he previously said he would not resign over the affair.
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