Paetz continues to deny the allegations against him
Celebrating mass in Poznan Cathedral on Thursday, in an annual liturgy for priests during which they renew their priesthood oaths, the archbishop said he had submitted his resignation for the "good of the church".
"The Holy Father accepted my resignation," he said.
He repeated his view that he had fallen victim to misinterpretations of his "kindness and spontaneity".
Underground tunnel
Archbishop Paetz has been accused by fellow priests of paying night visits to the lodgings of seminarians, cuddling up to young clerics in public and using an underground tunnel to pay unannounced visits to his targets.
He is the highest-ranking prelate to be brought down by a scandal of this kind since Austrian Cardinal Hans Hermann Groer was forced to give up all his duties in 1998, amid allegations that he had molested young boys.
The Vatican confirmed that the Pope had accepted the archbishop's resignation and named as his successor Monsignor Stanislaw Gadecki, 52, an auxiliary bishop in the town of Gniezno.
Last week in an annual letter to priests, the Pope denounced the "sins of our brothers" which brought scandal upon the Church and made the laity suspicious of even the "finest" priests.
He said these brothers had succumbed to "the most grievous form of evil at work in the world".
Vatican probe
A major paedophile scandal has engulfed the Roman Catholic Church in the United States, while other cases of sexual abuse and harassment involving the clergy have also recently come to light in Ireland and Australia.
Local priests in Poznan are reported to have waged a long campaign to have Archbishop Paetz removed from office and finally succeeded in getting the Vatican to send an investigative team in November.
Newspapers said the team had found no direct evidence of Archbishop Paetz abusing priests but concluded he had indulged in "inappropriate behaviour".
In a 17 March letter read in Poznan churches, the archbishop wrote: "I deny all the information published by the media and I assure you that it is a misinterpretation of my words and behaviour."