Physician Lisa Bardack examined the 68-year-old Clinton at her home in Chappaqua, New York, after she was forced to leave the ceremony at Ground Zero, a campaign aide said.
Video footage showed the candidate stumble as she was helped into her vehicle, and she needed to be held up on both sides by members of her entourage.
"Secretary Clinton has been experiencing a cough related to allergies. On Friday, during follow-up evaluation of her prolonged cough, she was diagnosed with pneumonia," Bardack said in a statement released by Clinton's campaign.
"She was put on antibiotics, and advised to rest and modify her schedule. While at this morning's event, she became overheated and dehydrated. I have just examined her and she is now re-hydrated and recovering nicely."
The former secretary of state was at the high-profile ceremony at Ground Zero in Manhattan for 90 minutes and greeted some family members of those killed in the deadly terror strikes 15 years ago, her campaign said in a statement.
"During the ceremony, she felt overheated so departed to go to her daughter's apartment, and is feeling much better," the statement said.
An AFP journalist at the ceremony noted that Clinton, dressed in a navy suit and white blouse, was greeting people as she left and did not appear to be rushing out. She walked out accompanied by an aide at her elbow.
However, a video posted on Twitter showed Clinton seeming unsteady as she waited to get into a black van. She appeared to stumble as she was helped into the vehicle, held up on either side by members of her entourage.
It was a humid day in New York, with temperatures around 82 degrees Fahrenheit (28 Celsius).
Clinton reappeared a few hours later, apparently recovered as she walked out of her daughter Chelsea's home. She smiled for the media and posed for pictures with a young girl before departing in a vehicle for her home in Chappaqua.
