Ibrahim al-Qaraghuli was one of three suspected militants who have gone to trial for the killings.
The other two - Walid al-Kartani and Kazim al-Zubaie - were found not guilty for lack of sufficient evidence, but it was not immediately clear whether they would be released from custody. All three men are Iraqis and have been in custody for at least a year.
Tuesday's court hearing was held in the fortress-like Law and Order Complex that was built last year in eastern Baghdad as part of a U.S. push to establish rule of law in Iraq and protect judicial officials from attacks by insurgents and criminal gangs.
Al-Qaraghuli, who wore a prison jumpsuit, lowered his head Tuesday but remained silent when he heard the verdict read by chief judge, Munther Raouf Haadi.
The killing of the three 101st Airborne Division soldiers was one of the most brazen attacks against U.S. forces since the Iraq war began in 2003.
The three were ambushed June 16, 2006 while at an isolated checkpoint near the Euphrates River. The brazen attack came during a time of particularly intense fighting in predominantly Sunni areas just south of Baghdad where al Qaeda fighters were active. At the time, the area was known as the Triangle of Death.
David J. Babineau, 25, of Springfield, Mass., was found dead at the site of the checkpoint. The two other 101st soldiers were kidnapped, sparking a massive search effort by the military.
The mutilated bodies of Pfc. Kristian Menchaca, 23, of Houston and Pfc. Thomas Tucker, 25, of Madras, Ore., were found three days later near a power station, not far from the checkpoint.
It took crews several hours to recover the bodies because they had been tied together and booby-trapped with roadside bombs planted throughout the area.
An al Qaeda linked group later posted a Web video showing the bodies of the two soldiers being dragged behind a truck, then set on fire.
The evidence against the three included fingerprints collected from the truck, which was later found abandoned, along with written testimony from villagers who witnessed the dragging incident, according to U.S. military investigators.
Al-Kartani and al-Qaraghuli were arrested on separate days in July 2006 during security sweeps in the area. Al-Zubaie was detained a year later.
The U.S. military has said at least one other suspect has been killed.
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