Former Baath party official Abdul-Ghani Abdul-Ghafur also received a death sentence at the end of the trial, which began in August 2007. He shouted, "Down with the Persian-U.S. occupation!" as the sentence was read.
"Shut up, you dirty Baathist," snapped chief judge Mohammed Oreibi al-Khalifa, referring to Saddam's mostly Sunni Baath party.
The trial was one of five convened against former leaders of Saddam's regime, which was ousted in the 2003 U.S.-led invasion. Two are still ongoing.
In the first trial, Saddam was convicted of crimes in the killing of more than 140 Shiites after an assassination attempt against him in Dujail.
He was hanged in December 2006.
After Saddam's defeat in the 1991 Gulf War, Shiites in southern Iraq and Kurds in the north rose up against his regime and seized control of 14 of the country's 18 provinces. U.S. troops created a safe haven for the Kurds in three northern provinces, preventing Saddam from attacking.
But Saddam's troops marched into the predominantly Shiite south and crushed the uprising, killing tens of thousands of people.
In this trial, four defendants received life sentences, six were sentenced to 15 years in prison and three were acquitted.
Among those who received a 15-year sentence was former Defense Minister Sultan Hashim Ahmad al-Tai.
He has also been sentenced to death for the Kurdish crackdown. But al-Tai's execution has been delayed because of an outcry from fellow Sunnis who believed the sentence was too harsh.
After the end of the court session, al-Khalifa told reporters that he is convinced the verdicts were "fair and just."
He added that some defendants were given 15 years instead of life sentences because they showed remorse and apologized for their role in crushing the uprising.
"The existence of anti-government protests, even if a few protesters were carrying personal weapons, does not justify the use of tanks and helicopters to kill people at random," al-Khalifa said. "It took us 75 sessions to reach the verdicts in this case while Saddam's Revolutionary Court needed two minutes to try and sentence a defendant to death."
A lawmaker for the movement loyal to anti-U.S. Shiite cleric Muqtada al-Sadr hailed the verdicts.
"This day is the day of examination and punishment," Fawzi Akram told AP Television News. "In the (Shiite) uprising, the Iraqi people made heavy sacrifices. Crimes unprecedented in modern Iraqi history were carried out, including killings and random raiding and mass killings, with no regard for law or justice."
Al-Majid and former Foreign Minister Tariq Aziz are also on trial for allegedly orchestrating the bloody repression of Shiite riots after the 1999 assassination of al-Sadr's father.
Aziz also faces charges in another trial under way for officials accused in the 1992 execution of dozens of merchants accused of manipulating food supplies to drive up prices during hard economic times under U.N. sanctions.