A witness told The New York Post the former Secretary of State's knees buckled and she lost a shoe as her aides led her away from the event.
Clinton, who has been dogged by accusations of poor health, later emerged from her daughter's apartment smiling and telling waiting reporters she was fine. "I'm feeling great, it's a beautiful day in New York," she said.
She was reportedly heading home to Chappaqua in New York, CNN reported.
A campaign spokesman said Clinton left the ceremony, which was also attended by Donald Trump, early because she "felt overheated". The temperature was around 27C.
"Secretary Clinton attended the September 11th Commemoration Ceremony for just an hour and 30 minutes this morning to pay her respects and greet some of the families of the fallen," spokesman Nick Merrill said.
"During the ceremony, she felt overheated so departed to go to her daughter's apartment, and is feeling much better."
Clinton has been plagued by rumours that her health is failing, with Trump repeatedly questioning whether she has the "stamina" to serve as president.
Last month, a zoomed-in photo of a Secret Service agent standing beside Clinton and holding an unidentifiable cylindrical object went viral.
Right-wing social media users immediately concluded that the agent was holding an autoinjector containing Diazepam, a muscle-relaxant drug used to treat seizures and anxiety, for Clinton.
In December 2012, Clinton suffered a concussion and shortly afterwards developed a blood clot.
In a letter released by her doctor in July, Clinton was described as being in "excellent health" and "fit to serve" in the White House.
Clinton's speech at a campaign rally earlier this month in Cleveland was interrupted by a coughing spell. During the speech, she quipped, "Every time I think about Trump I get allergic." She then resumed her speech.
But the episode fuelled speculation from conservative political quarters about her health. Trump supporters have been tweeting unsubstantiated theories regarding Clinton's health under the hashtag #HillarysHealth.
PRESIDENT OBAMA KICKS OFF COMMEMORATIONS
Meanwhile, US president Barack Obama observed the sombre anniversary with a moment of silence in the Oval Office at 8.46am local time.
That's the time when the attacks began on that sunny day in 2001 - when a hijacked aeroplane slammed into the north tower of New York City's World Trade Centre.
Afterwards, Obama arrived at the Pentagon, where he laid a large wreath at the beginning of a memorial service.
"In the face of terrorism, how we respond matters," President Obama said in his weekly address. "We cannot give in to those who would divide us. We cannot react in ways that erode the fabric of our society."
The al-Qaeda attacks killed 2753 people in New York, 184 at the Pentagon in Washington D.C. and 40 on Flight 93 - which had also been headed toward the US capital until passengers and crew staged a rebellion and the hijackers crashed it into a field in Pennsylvania.
The service held at the September 11 memorial also paused to mark the moment when the second plane hit the South Tower. Other moments of silence will take place when each tower fell, as well as the attack on the Pentagon and Flight 93.
In New York, police and relatives of those killed in the World Trade Centre began the annual reading of the names of the victims at Ground Zero, now the site of the National 9/11 Memorial and Museum.
"It doesn't get easier. The grief never goes away. You don't move forward - it always stays with you," Tom Acquaviva, who lost his son, Paul Acquaviva, said as he joined over 1000 victims' family members, survivors and dignitaries at ground zero under an overcast sky.
For Dorothy Esposito, too, the 15 years since she lost her son, Frankie, is "like 15 seconds".
James Johnson, a retired New York City police sergeant who is now police chief in Forest City, Pennsylvania, was there for the first time since he last worked on the rescue and recovery efforts in early 2002. "I've got mixed emotions, but I'm still kind of numb," he said. "I think everyone needs closure, and this is my time to have closure."
New York Mayor Bill de Blasio wrote on Twitter: "September 11, 2001 touched every single NYer, but the terrorists did not prevail, because 15 years later we are strong, and we are unified."
George W. Bush, who was president at the time of the attacks, was not expected to attend either ceremony in New York or Washington.
Instead, his office said he will go to church in Dallas, Texas, and then attend the Dallas Cowboys home opener against the New York Giants, where he will take part in the ceremonial coin toss with two New York police officers who were at Ground Zero on 9/11.
The commemorations came as health experts revealed the devastating ongoing impact of the attacks.
The Guardian reported that the death toll among those sickened by toxic dust and ash has reached at least 1000 and is predicted to eventually exceed the number killed in the attacks.
According to the paper more than 37,000 are officially recognised as sick due to their exposure to debris that spread from the wreckage of the World Trade Centre towers.
"Within the next five years we will be at the point where more people have died from World Trade Center-related illnesses than died from the immediate impact of the attacks," Dr Jim Melius, a doctor at the New York State Labourers Union, told the paper.
"There are a lot of people who are very, very ill with lung disease who will see at least 10 years taken from their normal life span," he said, "and we are already seeing many more premature deaths occurring, and among younger people, from the cancers. There is going to be a new generation of widows and widowers."
