Harris, the Democratic presidential nominee and Trump, her Republican rival in the November 5 US presidential election, shook hands and exchanged a few words despite their a contentious debate the night before, then lined up for the commemoration.
Trump's running mate, Senator JD Vance of Ohio, also attended.
Instead of formal remarks, the ceremony at the "ground zero" site where planes brought down the World Trade Center's twin towers included wives, husbands, sisters, brothers and grandchildren reading the names of family members killed 23 years ago.
The annual rite marks the suicide attacks by Islamist militants that hit Manhattan, the Pentagon and a Pennsylvania field.
"Richard J O'Connor. We will always love and miss you," a small red-headed boy said of his grandfather, who was killed in the World Trade Center that morning.
A bagpipe and drum processional was accompanied by New York City's fire and police departments and Port Authority honour guards.
The national anthem was performed and moments of silence were held at the times each target was struck.
The current and former US presidents have exchanged words at a 9/11 memorial ceremony in New York. (AP PHOTO)
Former New York mayor Michael Bloomberg also attended, standing between Biden and Trump.
After New York, Biden and Harris were flying to Shanksville, Pennsylvania, where passengers on United Flight 93 overcame the hijackers and the plane crashed in a field, preventing another target from being hit.
Then the president and vice president will head back to the Washington DC area to visit a memorial at the Pentagon.
"On this day 23 years ago, terrorists believed they could break our will and bring us to our knees. They were wrong. They will always be wrong. In the darkest of hours, we found light. And in the face of fear, we came together - to defend our country, and to help one another," Biden said in an early morning statement.
Trump, who also plans to visit the Pennsylvania memorial, told Fox News on Wednesday: "It was very, very sad, horrible day. There's never been anything like it."
Biden earlier issued a proclamation honouring those who died as a result of the attacks, as well as the hundreds of thousands of people who volunteered for US military service afterwards.
"We owe these patriots of the 9/11 generation a debt of gratitude that we can never fully repay," Biden said, citing deployments to Afghanistan, Iraq and other war zones as well as the capture and killing of Osama bin Laden and his deputy.
US congressional leaders on Tuesday posthumously awarded the Congressional Gold Medal to 13 service members who were killed in the August 26, 2021 suicide bombing at Kabul's airport during the chaotic US withdrawal from Afghanistan.
