His final day in the United States started with an eerie and sombre visit to the symbol of the September 11 attacks by al Qaeda and ended with a religious service at the pre-eminent shrine of baseball, "the great American pastime".
At Ground Zero, now a gaping crater, he prayed for the victims, their families and an end to hate and violence.
In the most intense public portion of his first papal visit to the United States, Pope Benedict blessed the area - considered hallowed ground by many - and comforted each of 24 special guests as a lone cellist played sombre music.
They were 16 relatives of people killed when the jets hit the towers and eight survivors - four World Trade Centre workers and four first responders who rushed to help. Some were Catholics and kissed his ring as they told their story.
Fog shrouded tops of towering skyscrapers as the Pope, 81, dressed in a long white wool coat against the chill wind and damp, read a prayer for those who died at Ground Zero, the Pentagon and on United Flight 93, which crashed in Pennsylvania after passengers overwhelmed the hijackers.
"God of peace ... turn to your way of love those whose hearts and minds are consumed with hatred," he said, after blessing the site with holy water and lighting a large candle symbolising sacrifice and resurrection.
"Grant that those whose lives were spared may live so that the lives lost here may not have been lost in vain. Comfort and console us, strengthen us in hope, and give us the wisdom and courage to work tirelessly for a world where true peace and love reign among nations and in the hearts of all."
It was eerily silent at the construction site 75 feet (25 metres) below street level at the geological bedrock that supports Manhattan's skyscrapers. Some survivors cried.
One of those attending was John McLoughlin, a Port Authority of New York and New Jersey Police officer who was one of the last people pulled out and who was the focus of the Oliver Stone movie "World Trade Center" starring Nicolas Cage.
