The Democratic presidential candidate’s campaign said earlier she had left the event in New York because she had “felt overheated” and had gone to her daughter’s apartment.
Hillary Clinton’s Republican opponents have queried her physical fitness.
Doctors say Hillary Clinton made a full recovery from surgery she underwent in 2012 for a blood clot.
Her personal doctor, Lisa Bardack, said last month Hillary Clinton was “in excellent health and fit to serve as president of the United States”.
The Clinton campaign has accused opponents of pushing a “deranged conspiracy about Clinton’s health”.
Hillary Clinton is 68. Her rival Republican candidate Donald Trump is 70.
Emerging from her daughter’s home, Hillary Clinton said: “I’m feeling great. It’s a beautiful day in New York.”
Hillary Clinton later left for her home in Chappaqua, New York, according to her campaign.
A video posted on Twitter purports to show Hillary Clinton being supported by aides at the 9/11 ceremony before being helped into her van.
The statement from the Clinton campaign said: “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.
“During the ceremony, she felt overheated so departed to go to her daughter’s apartment, and is feeling much better.”
The weather was warm and humid in New York on September 11, and there was a breeze during the ceremony, the Associated Press reports.
Hillary Clinton came to the ceremony fresh from a political storm over comments she made about Donald Trump’s supporters at a fundraiser on September 9.
On September 10, she had apologized for suggesting half of the Republican’s supporters were “deplorables”.
Hillary Clinton is next due to appear on the Ellen DeGeneres Show on September 14 and attend a rally in Las Vegas on the same day.
Services marking the 15th anniversary of the 9/11 attacks have taken place in New York and around the world.
Passions are high just over two weeks before the first election debate between Hillary Clinton and Donald Trump on September 26.
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