The royal visit to lower Manhattan came at a time of tensions between the United Kingdom and the United States, with President Donald Trump having criticised Prime Minister Keir Starmer for what he says is his lack of help in the US and Israel's war with Iran.
Michael Bloomberg, a former New York City mayor, walked the King and Queen to one of the reflecting pools that outline the footprints of the 110-storey towers destroyed when al-Qaeda militants flew two planes into the skyscrapers.
Charles laid a bouquet of white lilacs, daffodils and peonies on the bronze parapet surrounding the pool, engraved with the names of all the fatal victims of the attack.
A note accompanying the flowers, in the King's handwriting, read: "We honour the memory of all those who so tragically lost their lives on 11th September 2001, and stand in enduring solidarity with the American people in the face of such profound loss. Charles R Camilla R."
The three stood silently before heading into a canopy to meet with guests including relatives of some of the nearly 2800 people killed in New York that day.
The King also spoke with New York City mayor Zohran Mamdani at the ceremony and met the governors of New York and New Jersey.
The UK was an immediate and staunch supporter of the US response to the 9/11 attacks, which also included a plane that crashed into the Pentagon and another downed in a Pennsylvania field by passengers who battled hijackers, launching a years-long "war on terror".
King Charles referred to September 11 during his speech to the US Congress on Tuesday, saying "we answered the call together".
Charles stressed the historical military and cultural ties between the UK and the US, as well as the importance of NATO at a time when Trump has been critical of the military alliance's reluctance to provide military assistance in the US-Israeli war on Iran.
The royal couple's four-day state visit celebrates the 250th anniversary of the United States' declaration of independence from British rule.
After the 9/11 memorial, King Charles will head to Harlem to visit a grassroots community organisation that created a sustainable after-school urban farming initiative in an effort to combat food insecurity.
Such projects have been a passion of the King for decades.
Meanwhile, Camilla was due to celebrate the 100th birthday of AA Milne's fictional character Winnie-the-Pooh on behalf of her charity, The Queen's Reading Room, which Buckingham Palace is calling a "literary engagement" event.
The Queen's New York Public Library visit will include 100 guests from the UK and US literary, cultural and publishing worlds, the palace said.
Camilla will then meet with representatives of domestic violence charities in the area.
