Reverend Archimandrite Zacchaeus, who represents the Orthodox Church in America to the Moscow Patriarchate, led the service at the Church of St. Catherine the Great Martyr in both English and Church Slavonic.
U.S. Ambassador to Russia John Beyrle led a prayer for those killed in the hijacking and subsequent crashing of four U.S. planes, along with the victims in the 2002 theater-siege in Moscow, Beslan in 2004, London in 2005 and Madrid in 2004.
"Unfortunately this sad list of cities is only growing. All these people died at the hands of fanatics," he said.
A senior Foreign Ministry official conveyed a message to the congregation from Foreign Minister Sergei Lavrov, remembering the "thousands of peaceful people of many nationalities" who died in the 9/11 attacks.
"We grieve together with their close ones, their compatriots, and with those who were brought face to face with the horrors of terrorism," said the message read out by Igor Neverov, who heads the ministry's North American department.
"These evil acts are akin to the genocide in which civilians in South Ossetia fell victim," Lavrov's message said.
The service was also attended by the head of Russian Railways, Vladimir Yakunin, and the head of the Central Election Committee, Vladimir Churov.
In the U.S., political rivalries have been put on hold, and Republican candidate John McCain and Democrat Barack Obama are set to pay a joint visit to Ground Zero in New York.
Almost 3,000 people died on September 11, 2001, when terrorists crashed planes into the World Trade Center's twin towers in New York City, a field in Shanksville, Pennsylvania, and the Pentagon in Washington.
