Pope Benedict XVI has visited Ground Zero, the scene of the 11 September attacks in New York in 2001, on the final day of his six-day visit to the US.
He prayed for the nearly 3,000 victims and their families and for an end to hatred and violence.
Among the small group of guests were 16 relatives of people killed when hijacked jets hit the towers.
The pope prayed for those who died at Ground Zero, the Pentagon and on United Flight 93 in Pennsylvania.
He then lit a tall candle at the pool and read out a special prayer.
After praying for the dead and their families, he said: ‘God of peace ... turn to your way of love those whose hearts and minds are consumed with hatred.’
‘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
The passage about those with ‘minds consumed with hatred’ has stirred controversy because some people interpreted it as a prayer for hijackers who were killed in the attacks.
Vatican officials have not interpreted the prayer but noted that Pope Benedict has in the past urged radicals to eschew violence and use only peaceful means.
Last month, al-Qaeda leader Osama bin Laden accused Benedict of being part of a ‘new crusade’ against Islam. The Vatican rejected the accusation.
The memorial service took place at the construction site, 25m below street level.
The Pope spoke with each of the 24 guests, some of whom were Catholics and kissed his ring as they stepped up to meet him.
After the visit to Ground Zero, the Pope was greeted by 55,000 people cheering and waving the Vatican's white and yellow flags at Yankee Stadium, in the end of his US visit.
Six day visit by Pontiff
Throughout his first papal visit to the US, Pope Benedict spoke out about the sexual abuse scandal that rocked the US Church and has cost it some $2bn in settlement payments with victims.
In a sermon at New York's St Patrick's Cathedral yesterday, he said he was spiritually close to the US Church as it deals with the aftermath of the scandal and cleanses and renews itself.
While addressing thousands of young people, the Pontiff recalled growing up under the Nazis. He said his teenage years had been marred by a sinister regime that thought it had all the answers.
The Pope urged young US citizens to avoid the snare of drugs and materialism and seek the truth about life.
In Washington on the first leg of the visit, the 81-year-old Pope met victims of sexual abuse by priests.
On his way to the US, he said, 'it is more important to have good priests than to have many priests.'
