A campaign spokesman confirmed that Clinton, 68, had suffered from overheating and left the ceremony early.
"Secretary Clinton attended the September 11th Commemoration Ceremony for just an hour and thirty 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."
The incident quickly renewed attention to Clinton's health. Her rival, Republican Donald Trump, has repeatedly questioned her well-being, saying that she doesn't have the "strength" or "stamina" for the presidency and accusing her of being "exhausted" and sleeping too much.
Neither Trump, who is 70, nor his aides responded immediately for requests for comment Sunday. But the attacks have intensified in the past month as unverified and often debunked theories about Clinton's health have floated around the Internet. And Sunday's incident prompted an avalanche of speculation on social media.
One individual familiar with the incident confirmed that Clinton felt ill and wobbly at the event.
And a former agent said that the detail’s movements show they had not planned for her to leave that early and had to make up some rushed security plans on the fly. The detail leader, normally in charge of sticking by her side at all times, had to leave her momentarily to open the door of her van.
"However, all details were reporting heat related matters/issues," the first individual said. "This is actually common and anticipated for events such as this."
Later, shortly before noon, Clinton was seen leaving daughter Chelsea's apartment. She hugged a child, waved and departed in her motorcade.
"I'm feeling great, it's a beautiful day in New York," Clinton said as she walked out of her daughter's apartment.
Clinton arrived at the memorial at 8:18 am and greeted Sen. Joe Manchin (D-W.Va.) and his wife as she exited her van, according to the pool.
"Hillary and I chatted for quite a while about our remembrances of 9/11/01 and our families," said Sen. Chuck Schumer (D-N.Y.), who also attended the ceremony, in an emailed statement. "It was pretty hot out there, but she seemed fine to me, and left on her own accord."
Reporters traveling with Clinton became aware about 9:36 a.m. that she was no longer in the place where she had been standing. By 9:48 a.m., her campaign confirmed that Clinton had left the viewing area but offered no more details until about 11 a.m.
Clinton's daughter lives on East 26th Street, in the Gramercy neighborhood of lower Manhattan -- about a 15-minute drive from Ground Zero.
Just before noon, it was 82 degrees and humid at Ground Zero, though it was probably a bit cooler when Clinton left two hours earlier. Reporters traveling with Clinton could not see her directly, but the politicians around her were all standing and packed tightly together. It was not clear if she was standing in direct sunlight, but there was not much shade anywhere at the service.
Rep. Joe Crowley (D-N.Y.), who stood near Clinton at the ceremony, said “everything seemed normal when I greeted her. She gave me a big hug and a kiss.”
“I’m not shocked to hear she got a little light-headed because of the stifling heat,” Crowley said, adding that he and others were sweating through their shirts. “I needed a gallon of water myself.”
Crowley said it is unfortunate that this episode will feed into conspiracies about Clinton’s health. He said anyone could have been similarly affected and Clinton tends to be held to her own “demigod” status.
Clinton walked out of Chelsea Clinton’s apartment wearing the same dark blue suit and sunglasses she had been wearing at the memorial. She waved, smiled and paused to talk to a young child.
“Yes, thank you, very much,” Clinton responded when asked by a reporter whether she was feeling better.
Clinton has been generally healthy as an adult, with the exception of clotting in one leg in 1996 and a concussion and associated health problems from a fall in December 2012. But she has been repeatedly criticized by conservatives and accused of hiding more serious health issues.
Former New York City mayor Rudy Giuliani, a close adviser to Trump who is regularly at his side on the campaign trail, said last month that he thinks Clinton is "tired" and "looks sick."
"What you've got to do is go online," Giuliani said on "Fox News Sunday” in late August, accusing the media of hiding information about Clinton's health. "So, go online and put down Hillary Clinton illness, take a look at the videos for yourself."
If he wins, Trump would become the oldest president ever elected. In December, Trump released a four-paragraph letter signed by Dr. Harold N. Bornstein of Lenox Hill Hospital in Manhattan that contained few specifics but declared that Trump would "be the healthiest individual ever elected to the presidency."
A coughing episode on Labor Day, meanwhile, prompted a fresh round of questions about Clinton’s health. During a speech during a festival in Cleveland, Clinton started coughing repeatedly at the outset of her remarks, took several sips of water and a lozenge and continued to sound hoarse as she spoke. Later that day, she interrupted a question-and-answer session with reporters in the back of her plane after she started coughing. Clinton told reporters her condition was due to “seasonal allergies.”
The 2012 episode led to a brief hospitalization for a blood clot in Clinton’s head. Details on Clinton’s condition were initially hard to come by, but her State Department office eventually provided extensive medical information.
Clinton wore special corrective glasses for some months afterward, and her husband, former president Bill Clinton, told an audience in 2014 that it had taken about six months for his wife to recover fully. Clinton herself has said she was surprised by the illness, because she had not experienced anything like it before.
Clinton’s campaign released a memo from her personal physician, Lisa Bardack, last summer, pronouncing the candidate healthy and suffering no lasting effects from the concussion.
The 2012 concussion caused concern among Clinton friends and supporters who hoped she would make a second run for the presidency, and some of whom predicted correctly that the episode would fuel speculation that Clinton was too frail to be commander in chief.
Her campaign dismisses any suggestion that the candidate, who is 68, is not up to the job, while suggesting that the speculation is an example of a sexist double standard not applied to male candidates.
Clinton seemed upbeat and sometimes jovial as she engaged with reporters several times on her campaign plane last week. However, as rumors have mounted about Clinton’s health in recent weeks, her running mate, Sen. Tim Kaine of Virginia, has inserted a short section into his speeches about how much stamina she has.
During a keynote address Saturday night at a Human Rights Campaign dinner, Kaine said he is “amazed when Donald Trump makes fun of Hillary Clinton’s stamina and energy because I got added to the ticket 100 days out, and I’m already getting lapped by her.”
“I can’t imagine the stamina and energy it takes to run this campaign for 18 months,” Kaine added. “This is one determined lady.”
Sarah Dirkes, Jamie Relle, Caitlyn Cockran, and Elizabeth Ward were sitting at brunch at the Black Barn, a restaurant next door to Chelsea Clinton's building, when they saw Hillary Clinton emerge at about 11:45 a.m.
"She looked fine," said Ward, who was just finishing up her brunch.
"Great sunglasses," added Dirkes.
A little girl also ran up to Clinton and asked for a photo with her. The Democratic nominee obliged, and waved to other brunchers at Black Barn before getting in a car and departing.
Gearan reported from Washington. Kayla Epstein and Philip Bump in New York, and Jenna Johnson, Carol D. Leonnig and John Wagner in Washington contributed to this report.