Police estimated the crowd which filled St Peter's Square and Via della Conciliazione, the broad avenue leading to the holy city, at more than 150,000.
Some bore banners of support for the embattled head of the Roman Catholic Church saying "Together with the Pope" and "Your Holiness, you are not Alone, the whole Church is with you."
The demonstration of support was organised by the Italian Episcopal Conference, two days after Benedict's return from a four-day visit to Portugal which was marked by huge crowds.
"Today you show the great affection and profound closeness of the Church and the Italian people to the pope and your priests... because, in the commitment to spiritual and moral renewal, we can always do better," Benedict said, addressing the crowd from the balcony of his Vatican apartment.
"The real enemy to fear and to fight is sin, spiritual evil, which at times, unfortunately, also infects members of the Church," he said.
In what may yet be seen as a watershed in his battle against the Church's biggest crisis in decades, a penitent pope said last week en route to Portugal that the problems it faced came not from its enemies, but from sin within the institution itself.
Cardinal Angelo Bagnasco, president of the Italian Bishops Conference and archbishop of the northern city of Genoa, led a group prayer focused on the meaning of purification, solidarity, forgiveness and justice.
The Church, "faithful to its mission", must be "purified of the sins of its sons", Bagnasco said.
Tens of thousands of pilgrims, made up of many Catholic associations, arrived in Rome aboard hundreds of chartered buses and special trains.
"We came from all over Italy to Saint Peter's to express our affection in a moment that is so difficult for him and the entire Church," said Paola Dal Toso, head of one of the associations that organised the rally.
"I am here to support the Holy Father in this difficult moment for the Church. He's a good pope who has known how to react to the paedophilia scandals," said Cristian Papachioli, a 25-year-old student priest.
Chiara, a 37-year-old from the northern Italian city of Piacenza, said: "We are lucky to have such a committed pope, it's a blessing."
The faithful had gathered beneath a cloudy sky below the pope's balcony since early morning, to pray with him during the Regina Coeli, celebrated each Sunday in the weeks ahead of Pentecost.
"I thank you with all my heart, dear brothers and sisters, for your warm presence," Benedict told them.
The Church has for months been embroiled in a series of sex abuse scandals amid allegations that the Vatican had protected paedophile priests from prosecution in several European countries and the United States.
The pope's comments that the Church was alone culpable were effectively a reversal of earlier Vatican attempts to blame media sensationalism for its problems and won praise from Vatican watchers.
The Holy See said the turnout in Portugal has been a strong public response to attacks on the leader of the world's 1.2 billion Roman Catholics over his handling of the paedophile crisis.
"The vitality of the people's faith demonstrates great hope, despite internal and external difficulties" facing the Church, Vatican spokesman Federico Lombardi said at the end of the visit.