Another plane, United Airlines Flight 93, crashed in a field in Shanksville, Pennsylvania.
It is believed hijackers were planning to aim that aircraft at the Congress or White House in Washington DC before it went down, killing all 40 people aboard.
Cockpit voice recordings of the hijackers and mobile phone calls from those aboard to loved ones indicate passengers tried to fight their way into the cockpit to regain control before the plotters nosedived the plane.
President Trump praised the passengers’ “incredible valor” and said their revolt was “the moment America fought back”.
He said: “A band of brave patriots turned the tide on our nation’s enemies and joined the immortal rank of American heroes.”
Donald Trump is the third sitting president to attend the crash site, 70 miles south-east of Pittsburgh.
Senator John Cornyn, a Texas Republican, was among those who noted this is the first year that Americans born after the attacks will be old enough to enlist in the US military.
During remarks at the Pentagon, VP Mike Pence told audience members they “must learn the lessons of 9/11 and remain ever vigilant”.
The ceremony in New York was attended by New York Governor Andrew Cuomo, US ambassador to the United Nations Nikki Haley and Mayor Bill de Blasio, as well as former mayors Michael Bloomberg and Rudy Giuliani.
Relatives of victims read out the names of the dead, and moments of silence were observed at 08:46 and 09:03 to mark the times when passenger jets struck the two skyscrapers.
In the years since the attacks, cancer cases in lower Manhattan – especially among first responders who dug through the toxic rubble – have increased.
The 9/11 Victims’ Compensation Fund has paid out $4 billion to fund medical expenses for survivors of the terror attacks.
According to the World Trade Center Health Program, nearly 10,000 of them have had some form of cancer.
Tens of thousands of people inhaled fumes in the days after the attack, and the number of patients coming forward with tumors has increased in recent years, according to the fund.
America is remembering the victims of the 9/11 attacks in a series of memorials marking the 12th anniversary.
The 9/11 attacks killed 2,977 people in New York, the Washington DC area and Pennsylvania.
In New York, families of the victims read the names of each person who died at the World Trade Center.
President Barack Obama was set to attend a memorial outside the Pentagon, but no speeches have been planned by politicians.
The attacks led to a long war in Afghanistan and created an expansion of government surveillance powers that have recently been the subject of intense debate.
A separate memorial was held outside Shanksville, Pennsylvania, honoring the passengers and crew of United Flight 93. They struggled with the hijackers of the plane, preventing it from hitting its intended target, believed to be the White House or the US Capitol building.
All 33 passengers and seven crew members on the flight were killed after the plane crashed into a field about 75 miles south-east of Pittsburgh.
“No matter how many years pass, this time comes around each year, and it’s always the same,” Karen Hinson, who lost her brother, Michael Wittenstein, in New York, told the Associated Press news agency. His body was never found.
America is remembering the victims of the 9-11 attacks in a series of memorials marking the 12th anniversary
More than 1,000 people gathered on Wednesday at the National September 11 memorial plaza in New York City to read the names of all those killed in the 2001 and 1993 attacks on the building.
Bagpipes and a youth choir began the proceedings, held around two reflecting pools that stand in the footprint of the destroyed towers.
“To my nephew Michael Joseph Mullin, we miss you and think of you every single day,” said one of the 250 people chosen to read names, many of them family members of the victims.
“You’re gone but not forgotten,” another woman said of her lost cousin.
The reading was paused for several moments of silence, including 8:46 local time, when the first plane hit the North Tower; when the second plane hit the South Tower; when each building fell; and when the third and fourth planes hit the Pentagon and the field outside Shanksville.
A number of other cities held memorial services on Wednesday.
Builders are meanwhile putting the finishing touches to the new World Trade Center tower and a museum dedicated to the attacks.
One World Trade Center is now the tallest building in the Western hemisphere, its spire reaching to 1,776ft, a symbolic number alluding to the year of the US Declaration of Independence.
On Tuesday, a groundbreaking ceremony was held for what will be a visitor centre on the site of the Flight 93 national memorial park.
The building, expected to open in late 2015, will be broken in two where the plane flew overhead. Visitors have already left 35,000 tributes at the site.
Osama Bin Laden and al-Qaeda claimed responsibility for the 9/11 attacks, in which 19 hijackers also died when they seized control of four planes, crashing three of them into their intended targets.
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