Waddah Ismail al-Shaikh, a former prison warden, was shown sitting in a wheelchair and dressed in a hospital robe giving testimony over the killing of 148 men and youths from the Shia village of Dujail after an attempt on Saddam's life.
The court also saw a brief video clip of Saddam in Dujail when the trial resumed after a 40-day break.
Al-Shaikh, who has since died, testified that about 400 people, including women, children and old people, were rounded up after Saddam's convoy came under fire in Dujail in July 1982.
"The troops took orders from Barzan, they spread out through town and started arresting citizens ... including entire families," he said, referring to Barzan Ibrahim Hassan al-Tikriti, one of Saddam's three half-brothers and a former director of the feared Mukhabarat intelligence service.
In the video clip, Saddam was heard telling his security forces to "separate them and investigate them".
Al-Shaikh was warden of the notorious al-Hakmia prison in Baghdad, where most of the Shia were taken from Dujail.
The prison had a reputation for taking in political prisoners who rarely emerged alive.