He was one of several dozen Palestinians who hurled stones at soldiers during a protest against the barrier near the village of Nilin in the West Bank.
'Measure of justice'
The military court convicted the officer on Thursday for ordering the soldier to shoot. He resigned his field command shortly after the shooting but continued to serve elsewhere.
Both were convicted of unbecoming conduct, and the soldier was convicted of unlawful use of a weapon.
The soldier, a sergeant, has since completed his compulsory service. They have not been sentenced yet, but the charges carry a maximum punishment of three years in prison.
The human rights group B'Tselem, which distributed the video of the shooting, welcomed the court's ruling as "important, both as a measure of justice for the victim, as well as for the deterrent message it sends to soldiers and commanders".