Master Sergeant John E. Hatley, 40, was also found guilty of conspiracy to commit premeditated murder, but cleared on one count of obstruction of justice.
Hatley - who had entered a plea of not guilty - showed no emotion as the verdict from the eight-member jury was read out. He embraced his wife and soldiers from his former unit afterwards.
Hatley faces a maximum prison term of life without parole, and the court martial judge set sentencing for Friday, when the defendant was expected to testify for the first time. Hatley was accused of involvement in two separate incidents.
The first involved the shooting in January 2007 of a wounded detainee who medics said was close to death, a charge of which he was acquitted. The second shooting - of four blindfolded detainees - took place in late March or early April 2007 in or near southwest Baghdad.
Hatley was the highest ranking of three soldiers tried for killing the prisoners, who were shot "execution style" according to prosecutors.
Private Michael Leahy, a combat medic, and Sergeant First Class Joseph P. Mayo have already been found guilty and sentenced to life and 35 years in prison respectively, but could be paroled before then.
An exact date and location have not been determined for the second shooting, and the bodies, which witnesses said were dumped into a canal, have never been found.
"Where is the evidence?" demanded defence lawyer David Court, adding that the "ABCs" of murder convictions were absent because there was "no autopsy, no body, no cause of death." Court had told an eight-man court martial panel the government's case "nothing but a bunch of holes."
Responding for the prosecution, Captain Derrick Grace charged that Hatley had "decided to play judge, jury and executioner."
A raft of witnesses had testified to Hatley's leadership and personal qualities but Grace had insisted that "good soldiers don't murder people," and stressed the prisoners were "zip-tied, blindfolded and stationary."
Leahy and Mayo testified that the prisoners were shot point-blank in the back of the head with pistols. They had been captured a few hours earlier near a cache of assault rifles, a duffel bag of bullets, grenades and two sniper rifles.
Owing to a lack of evidence, they were not going to be processed however, and under rules of engagement the US patrol would normally have set them free. Instead, they were taken to a deserted site near a canal and killed. At the time, the unit was coming to terms with a fatal sniper attack on another sergeant a few weeks earlier.
The men were stationed at a highly exposed combat outpost in West Rashid, one of the most violent Baghdad neighbourhoods at the time. Repeated attacks on their position and the fact that prisoners were often set free had bred "frustration and fear" among the men, according to a witness at Mayo's trial.
He testified this week that after the killings, Hatley gathered his troops at their post and told them: "This was for our fallen soldiers."
But addressing the jury, Grace insisted Hatley had a duty to train his men in "what was right and what was wrong.
"He showed them what was wrong and it's your duty to show them what is right," the prosecutor concluded.