Benedict began the day with a Mass at St. Patrick's cathedral, the landmark Roman Catholic church on Fifth Avenue. The building was packed with cardinals and bishops, priests and nuns, who cheered him to mark the day he succeeded Pope John Paul II on April 19, 2005.
The German-born pope lamented that what he called "the joy of faith" was often choked by cynicism, greed and violence. Yet he drew an analogy to show how faith can overcome distractions and trials.
"The spires of St. Patrick's Cathedral are dwarfed by the skyscrapers of the Manhattan skyline, yet in the heart of this busy metropolis they are a vivid reminder of the constant yearning of the human spirit to rise to God," he said.
In America, he has said repeatedly, the religious intensity stands out in marked contrast to the tepid spiritual emphasis in his native Europe. That makes the U.S. a testing ground for him in his bid to counter secular trends in the world.
He also returned Saturday to the sex abuse scandal that he said has caused "so much suffering" for the American church, assuring his audience "of my spiritual closeness as you strive to respond with Christian hope to the continuing challenges that this situation presents."
It was the fourth time he has spoken of the scandal since beginning his first papal pilgrimage to the U.S. on Tuesday. While in Washington, he met with a small group of victims from the Boston Archdiocese, where the scandal boiled over in 2002. It was believed to be the first time a pope had met with victims of clerical sex abuse.
Vatican spokesman the Rev. Federico Lombardi, meeting with reporters Saturday, was asked if the scandal had dominated the agenda of the trip. He denied that, saying it was part of the central theme of the entire visit, "to give hope to the church in the United States."
Benedict later was driven to St. Joseph's Seminary in nearby Yonkers, for a rally with young Catholics and seminarians. Upon arriving he blessed about 50 disabled youngsters in the seminary chapel. Two small girls gave him a painting and a hug.
The pope got a hero's welcome at the youth rally from a festive crowd of 25,000, which burst into wild cheers when Benedict first acknowledged them from the stage. The shy theologian took time to reach out and shake hands with the ecstatic faithful in the front rows. The youngsters, meanwhile, sang "Happy Birthday" to him -- he turned 81 on Wednesday -- in his native German.
During his speech at the rally, Benedict reflected on the repression of his own youth under Nazism. He urged the young people and seminarians to carry on the faith while enjoying the liberties that they were fortunate to have.
"My own years as a teenager were marred by a sinister regime that thought it had all the answers," he said making a rare reference to his own life. "Its influence grew -- infiltrating schools ands civic bodies, as well as politics and even religion -- before it was fully recognized for the monster it was."
As the busy day wore on, Benedict showed signs of tiring. His secretary reminded him to give his greetings in Spanish at the youth rally.
"I forgot my Spanish," the pope said with a chuckle. And the crowd laughed.
At the end of the St. Patrick's service, Benedict was clearly moved when his top assistant, Vatican Secretary of State Cardinal Tarcisio Bertone, read a tribute for the third anniversary.
Benedict told the crowd of 3,000 that "I am deeply thankful" for the support they showed him, and for "your love, your prayers." The pope said that he, like St. Peter, was a "man with his faults."
The Rev. Michael Morris, a professor of church history at St. Joseph's Seminary in Yonkers, where a youth rally was organized for the pontiff Saturday, attended the Mass, and was among those cheering "Viva il Papa!" as Benedict passed by.
Morris, 47, credits John Paul's 1979 trip to the United States with drawing him toward the priesthood. He hoped Benedict's visit would inspire young men today to do the same.
"I think it was a wonderful boost for priests and religious," said Morris, speaking about the clergy, nuns and brothers in religious communities.
"We're encountering a whole new generation that is very fervent and in many ways more heroic," he said. "They've been through the scandal and they still want to serve."
Benedict himself, on the flight to America from Rome, said as he addressed the scandal that it was more important to have "good priests than to have many priests."
Upon arriving at St. Patrick's, the pontiff was met outside by Mayor Michael Bloomberg, while former Mayor Rudy Giuliani was inside.
Giuliani received Holy Communion during the service from one of the many clergy who offered the sacrament. That raised some eyebrows since Giuliani has been married three times and supports abortion rights. Catholics who divorce and remarry without getting an annulment from the church cannot receive Communion. Giuliani did receive an annulment after his first marriage.
Benedict blessed the cathedral with holy water before making his way to the altar of the landmark church. As the pope walked down the center aisle, nuns clutched at his robes, showing an enthusiasm for his presence that has spread among the general public.
The Vatican said the pope came outside from his residence on the Upper East Side on Friday night to greet a crowd of more than 500 people who had lined up for hours. He shook hands and blessed the crowd before returning inside.
On Sunday, the final day of his trip, the pope will visit ground zero to lead prayers, and later will celebrate a Mass at Yankee Stadium.
After the St. Patrick's service a roar went up from the crowd when the popemobile passed along Fifth Avenue, with people raising up their babies and others shooting pictures with cell phone cameras.
Daniela Rizzo brought her husband and their infant son from Connecticut.
"You can feel the energy," Rizzo said. "You can feel the faith."