The specially chartered Alitalia plane touched down at Rome's Ciampino airport at around 10:40 am (0840 GMT).
During the visit the pontiff paid a solemn visit to the site of the attacks of September 11, 2001, in New York before celebrating a huge mass at Yankee Stadium to close a historic US visit.
The pope pleaded for an end to sectarian hatreds as he prayed Sunday at Ground Zero, where the Twin Towers stood before hijackers rammed passenger planes into the skyscrapers, killing nearly 3,000 people.
"We ask you in your goodness to give eternal light and peace to all who died here," Benedict beseeched God after blessing the ground in all four directions. "Heal the pain of still-grieving families."
"Bring peace to our violent world ... turn to your way of love those whose hearts and minds are consumed with hatred," he said.
The pope had arrived at the former World Trade Center site in his white Mercedes-Benz popemobile, which drove slowly down a ramp that straddles the hole in the ground where the twin skyscrapers used to stand.
He descended some three-quarters of the way down the ramp and walked the final few meters (yards) to kneel in silent prayer.
Then, as a blustery wind blew, he lit a white candle within a glass tube, before intoning his prayer and blessing the ground.
As a solo cellist played, Benedict spoke to 24 survivors and relatives of those who perished in the attacks by Al-Qaeda hijackers.
Tom Riches, who carried his firefighter brother's body out of the site, had returned to be there with Benedict.
"Since that day, it's always been sacred to me," Riches told the Sun Sentinel newspaper. "Him blessing the ground there will make it official."
After the visit to Ground Zero, Benedict was greeted by 57,000 people cheering and waving white and yellow handkerchiefs at Yankee Stadium, a shrine to baseball which had been transformed into an open-air cathedral for a day.
"Most Holy Father, welcome to New York," said New York's archbishop, Cardinal Edward Egan from the purple, white and yellow platform dominated by the Vatican coat of arms set up on the baseball diamond, drawing a deafening roar from the crowd.
White-robed Roman Catholic clerics sat alongside a rainbow of baseball caps, and Asians and Hispanics prayed next to African-Americans and white descendants of European immigrants.
"In this land of freedom and opportunity, the Church has united a widely diverse flock in the profession of the faith," Benedict said in his homily, as sunshine cut through the layer of cloud that had blanketed New York since the morning.
The prayer of the faithful after the homily underscored the ethnic diversity so lauded by the pontiff as it was intoned in a half-dozen languages.
Benedict praised the United States as a land of religious liberty, and urged US Catholics to overcome differences and build on the foundation of the Church left by their forebears, many of them "immigrants whose traditions have so enriched the Church in America."
"Today's celebration is ... a summons to move forward with firm resolve to use wisely the blessings of freedom, in order to build a future of hope for coming generations."
The rapt audience interrupted the homily to applaud as the pope urged them to defend all life, "including the most defenseless of all human beings, the unborn child in the mother's womb."
Unlike his previous public appearances during his US visit, the 81-year-old pontiff made no mention in his homily of the sex abuse scandal that has rocked the US Church.
During his trip, Benedict took unprecedented steps to atone for decades of sexual abuse of young people by US priests, acknowledging the pain and damage caused by the scandal during a private meeting with five victims.
Even before arriving at Andrews Air Force base near Washington, the pontiff raised the long-running sex scandal, saying it had made him feel "deeply ashamed."
"The Church will do everything it can to heal the wounds caused by pedophile priests" and ensure "events of this kind are no longer repeated," he told reporters on the specially chartered Alitalia plane.
He mentioned the scandal in nearly every homily and speech he gave during the six-day visit, reiterating his shame, chastising the US church for its handling of the scandal, but calling on Catholics to stand by the church and clergy.
In another example of the German-born pope taking controversy by the horns, he added two events to an already busy itinerary, especially for an 81-year-old: a private meeting with Jewish leaders in Washington and the first visit to a synagogue on US soil.
Although far improved since the end of World War II, when Jews accused the Catholic church of turning a blind eye to the atrocities committed against them, relations between Catholics and Jews were strained recently when a controversial prayer, calling for Jews to be converted, was reintroduced.
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