Chief Warrant Officer Lewis Welshofer Jr was accused of torturing Iraqi Major General Abed Hamed Mowhoush, covering his head with a sleeping bag, binding him with electric cord and sitting on his chest until he died.
Welshofer, who avoided conviction on a stiffer murder charge, is the highest ranking officer to be found guilty over the death of a prisoner in Iraq.
A military jury found Welshofer guilty on Saturday night and he will be sentenced on Monday, said Judy Dutt, a spokeswoman at Fort Carson in Colorado where the court martial was held.
Welshofer was an interrogator at an Iraq detention center known as "The Blacksmith Hotel" in Al Anbar province, near the Syrian border in November 2003 when the US military was holding General Mowhoush.
The military believed General Mowhoush was a former close advisor of Saddam Hussein and a leader of the rising Iraqi insurgency at the time.
Prosecutors displayed gruesome pictures of General Mowhoush's body as they argued that Welshofer knowingly surpassed US military interrogation standards, ignored warnings and rebukes over his methods, which they called "torture", and did not fully inform his superiors of his techniques.
"He treated that general worse than you would treat a dog," said prosecuting attorney Major Tiernan Dolan said, according to media reports.
However, Welshofer's lawyers presented evidence in emails and other communications that interrogators had been urged to "take the gloves off" in their handling of prisoners, authorizing his techniques.
They also produced witness testimonies that General Mowhoush had been transferred into Welshofer's hands already badly beaten and with broken ribs, allegedly after brutal treatment by CIA officials and contractors, referred to in the trial as "civilian interrogators".
Welshofer's attorneys argued that the general had a heart condition that ultimately caused his death.
The five-day trial raised questions about whether the US military and CIA had officially sanctioned illegal torture in Iraqi detention facilities, under the guidance of the top general in Iraq at the time, Lieutenant General Ricardo Sanchez.
According to the New York-based Human Rights First, which monitors US detainee issues, over 100 detainees have died in US hands since the launch of the US war on terror in 2001, and 27 of them have been identified by the army as suspected or confirmed homicides.
However, the panel of six military officers restricted their judgement to Welshofer's own behavior in the Mowmoush case.
The highest-ranking US military official to be found guilty in the death of an Iraqi prisoner, Welshofer's conviction for negligent homicide and dereliction of duty could bring a maximum three years and three months in prison, Officer Dutt said.
Welshofer avoided a stronger murder conviction, which could have brought a sentence of life imprisonment without parole.