The jury of six Army officers convicted Chief Warrant Officer Lewis Welshofer Jr in the suffocation death of Iraqi Major General Abid Hamad Mawhush.
However, they found him not guilty on the more serious charges of assault and murder, which could have seen him given a life sentence.
Prosecutors accused Welshofer of using harsh techniques to try to get information from Mowhoush, describing them as "torture."
He was accused of placing Mawhush head-first in a sleeping bag, covering his mouth and sitting on his chest during an interrogation in November 2003.
Reaching their verdict late on Saturday night after more than six hours of deliberation, the military jury also found Welshofer guilty of negligent dereliction of duty.
He could face a sentence of up to three years in prison on the negligent homicide charge, military officials said.
Speaking after the verdict, defence lawyer Frank Spinner said the jury's decision recognised "the context in which these events took place".
He added: "It was a very difficult time in Iraq. There was confusion, and they were not getting clear guidance from headquarters."
Earlier, Spinner said in closing arguments that his client and other interrogators were under pressure from military commanders to come up with new techniques to replace ones that had proved ineffective.
The US military's reputation has been on the line in the wake of several cases of torture and abuse at the Abu Ghraib prison near Baghdad.
"He treated that general worse than you would treat a dog and he did so knowing he was required to treat the general humanely"
Major Tiernan Dolan,
Prosecutor Major Tiernan Dolan said the case was about a soldier failing to perform his duty to treat detainees humanely.
He painted a picture of a rogue interrogator who became frustrated with Mawhush's refusal to answer questions and escalated his techniques from simple interviews to beatings to simulating drowning, to killing him.
"He treated that general worse than you would treat a dog and he did so knowing he was required to treat the general humanely," Dolan said.
The treatment of the Iraqi general "could fairly be described as torture," he said.
Spinner, for the defence, had argued that the competing theory of how Mawhush died - suffocation or heart attack - should raise enough doubt to acquit his client.
"What he was doing, he was doing in the open, and he was doing it because he believed the information in fact would save lives," Spinner said.
Another defence attorney, Captain Ryan Rosauer, told the judge on Friday that officials believed Mawhush had information that would "break the back of the whole insurgency".
He also said Mawhush was believed to be helping in bringing foreign fighters into Iraq from across the Syrian border.
Sentencing in the case has been scheduled for Monday, after which the defence have said they will consider an appeal.