"We ... insistently beg forgiveness from God and from the persons involved, while promising to do everything possible to ensure that such abuse will never occur again," he said.
'Enemy of the church'
The 83-year-old pope, who has met abuse victims in the United States, Australia and Malta, also promised that the Church would enact stronger controls on choosing men who enter the priesthood.
"In admitting men to priestly ministry and in their formation we will do everything we can to weigh the authenticity of their vocation and make every effort to accompany priests along their journey, so that the Lord will protect them," he said.
Robert Mickens, Vatican correspondent for the weekly Catholic paper The Tablet in Rome, told Al Jazeera that while the pope may consider the issue to be over, it would be a different story for the victims.
"The pope today actually laid this at the foot of what he called the 'enemy' of the church - it's a kind of euphemism for the devil or Satan, that brought these things to light," he said.
"I don't think that's exactly what the victims of this abuse were expecting him to say."
Hundreds of cases of sexual and physical abuse of youths in recent decades by priests have come to light in Europe and the United States as disclosures encouraged long-silent victims to finally go public with their complaints.
Late last year, Ireland was rocked by two successive reports revealing widespread abuse mainly of boys by priests going back decades, coupled with the Church hierarchy's complicity in covering it up.
Benedict, in his earlier roles as an archbishop in Germany and later in his tenure at the helm of the Vatican morals office, has been accused by victim support groups of being part of a systematic cover-up by the church hierarchy of suspected paedophile priests.
Earlier this year a story in the New York Times newspaper published internal church documents regarding a paedophile priest in the US, surrounding accusations that the Reverend Lawrence Murphy abused up to 200 deaf boys from the 1950s to the 1970s.
Among documents the New York Times posted on its website was a 1996 letter about Murphy to Benedict, then the Vatican's senior doctrinal official, showing he had been informed of the case.
Benedict's deputy first advised a secret disciplinary trial but dropped the plan in 1998 after Murphy appealed directly to him for clemency. Murphy died later that year.
The Vatican has reacted defiantly to the suggestion that Benedict had been involved in a cover-up of Murphy's paedophilia, dismissing the allegations as "petty gossip".
But some groups have demanded he take responsibility for the Vatican as an institution.
Five bishops in Europe have already resigned over the scandal.
One has admitted sexual abuse, another is under investigation and three have stepped down over their handling of abuse cases.
The cases have hit the Catholic Church hard, with a poll two months ago in Germany showing that a majority of people had lost confidence in the Church and about a quarter of the country's Catholics are considering quitting.