In a pre-recorded address to the 50th International Eucharistic Congress in Croke Park, the Pope praised the church in Ireland for its heroic missionaries and its mighty contribution to the good of the world.
But he said the joy sparked by this legacy had been shaken in an appalling way by the abuse of children by priests, brothers and nuns.
Earlier, in his homily, the Papal Legate told the capacity congregation that the Lord heals the Church's wounds.
"Let us rejoice and be glad", Cardinal Marc Ouellet said. "We can rely on the Lord for a new beginning."
He said that God sustains the Church when it experiences limitations and failures and the Lord heals the Church's wounds and strengthens its members' love.
The grey morning skies over GAA headquarters cleared before Cardinal Ouellet proceeded to the alter with nine co-principal celebrants including Cardinal Seán Brady and Archbishop Diarmuid Martin.
In his address, Pope Benedict said much remains to be done on the path to liturgical renewal.
He said Ireland had been shaped by the mass at the deepest level for centuries and told the congregation that they were heirs to a Church that has been a mighty force for good in the world.
However, he said that force has recently been shaken in an appalling way by the revelation of the sins committed by priests against people entrusted to their care.
He said they abused people and undermined the credibility of the Church's message.
The Pope also announced that the 2016 International Eucharistic Congress will be held in Cebu in the Philippines.
The Pontiff received a standing ovation from the congregation after his message.
President Michael D Higgins and the Taoiseach Enda Kenny were among the congregation in Croke Park.
Earlier, there was a “Gathering Ceremony” featuring soprano Celine Byrne, composer Fr Liam Lawton, the Dublin Deaf Choir and the RTÉ Concert Orchestra among others.