According to the Defense Department statement, Speicher "was found dead at the crash site by Bedouins and his remains buried."
His fate had long remained a mystery, with some believing that the pilot was being held prisoner by then Iraqi president Saddam Hussein.
Acting on a tip from local Iraqis, US Marines stationed in the western Iraqi province of Al-Anbar in July recovered human remains from a desert grave and flew them to the United States for identification.
"The recovered remains include bones and multiple skeletal fragments," the statement said.
"Positive identification was made by comparing Captain Speicher's dental records with the jawbone recovered at the site. The teeth are a match, both visually and radiographically."
Iraqi citizens, including one who claimed to be present when Speicher was buried, led the Marines to the site, the Pentagon said.
President Barack Obama said the news was "a reminder of the selfless service that led him to make the ultimate sacrifice for our freedom."
"My thoughts and prayers are with his family, and I hope that the recovery of his remains will bring them a much needed sense of closure," he said in a statement released by the White House press office.
The top US commander in Iraq, General Ray Odierno, also issued a statement, offering his "deepest condolences to the Speicher family for the sacrifice Captain Speicher made in the service of his country."
"We reiterate our commitment to find and account for all military members and civilians who have gone missing in the service of our nation," said Odierno. "We will not stop until all are found."
-----------------------------------------------------------------------------------------------------------------------