Speaking at an interfaith ceremony at the Sept. 11 museum, the pope said there should be opposition to "any attempt to make us all the same." Rather, he encouraged all to "say yes to our differences, accepting reconciliation."
The service was held in a hall framed partly by an underground flood wall that became an emblem of resilience when it held fast after the attack. Standing nearby was the memento-covered steel column that was the last one removed from the wreckage.
Francis visited the museum as part of a three-city U.S. tour. He then departed for a break before resuming his day's busy schedule.
Francis sayd the world must look to its diversity of languages, cultures and religions and throw away "feelings of hate and revenge and rancor."
He also said that he was moved by visiting the site of the former World Trade Center's twin towers and by meeting relatives of some of the nearly 3,000 victims.
He asked God for eternal peace for those killed and he prayed to God to bring "peace to our violent world" and to "turn to your way of love" those who justify killing in the name of religion.
About a dozen religious leaders from the Jewish, Muslim, Greek Orthodox, Hindu and other faiths sat in chairs behind the Pope as he spoke at the interfaith ceremony.
Eighteen relatives of people who died in the attacks also heard the Pope's remarks.
Previously, Pope Francis' call for a world free of nuclear weapons drew applause from across the United Nations General Assembly — including from Iranian Foreign Minister Mohammad Javad Zarif.
Francis made the comments at the U.N. on Friday morning, his first stop in a daylong visit to New York.
Francis praised the recent Iranian nuclear deal in his speech to more than 100 world leaders and diplomats, saying it was proof that political will and patience can bring about fruits.
But Francis lamented that conflicts are raging elsewhere and that Christians and religious minorities, in particular, are being targeted. He called for a "grave summons" for world leaders to reflect on the innocents who are being slaughtered.