Muhammad Uraibi al-Khalifa cut off the microphone as Saddam attempted to speak. He then pointed to court bailiffs to escort the ex-president from the courtroom.
Saddam interrupted the proceedings by shouting a verse from the Quran.
Saddam shouted "fight them and God will punish them" in what appeared to be a call for members of his disbanded Baath party to continue fighting US forces in Iraq.
The judge then closed the proceedings to the media.
The judge told Saddam's six co-defendants that he had been patient with them, but they were obstructing the trial.
He said: "I allowed you to say what you want, but you've been making problems."
Hussain Rashid Muhammad, a defendant, stood up and shouted insults at the prosecutors.
When a bailiff forced him back into his chair, the former army commander punched him. The judge then had Muhammad thrown out and closed the session.
Saddam and his co-defendants have pleaded innocent to charges of genocide against Iraq's Kurdish population during a crackdown, code named Operation Anfal, in the late 1980s in which about 180,000 people were killed.
In Tuesday's hearing, the court heard a Kurdish woman, who testified from behind a curtain to conceal her identity, recount that women were raped and children died in detention during the 1988 campaign.
The woman, who spent six and a half months in detention, also said that Saddam's forces used chemicals against the detainees.
She said: "One evening, men walked into our detention hall, wearing [chemical] suits and masks and sprayed us with a material that caused the spread of lice and other diseases, like bronchial coughing. Many children died as a result."
The witness also testified that pregnant women were treated inhumanely. She said one woman had given birth in a toilet.
Fellow detainees helped her to "cut the umbilical cord with broken glass and the baby was wrapped in a grain sack."
She said all her family members disappeared in 1988 and were presumed dead.