The former Iraqi leader was ejected after he refused to sit down in protest at the appointment of judge Mohammed al-Oreibi al-Khalifah.
Mr Khalifah – a Shia Arab -- became chief judge after the government sacked his predecessor, Abdullahal-Amiri.
The Iraqi cabinet accused Amiri of bias for saying Saddam was not a dictator and for being too soft on the defendants.
Mr Khalifah immediately stamped his mark of proceedings, gesturing court officers to "Throw him out.".
Before being escorted out, Saddam told his fellow defendants: "You should leave too."
As he tried to start the session, defence lawyers said they would boycott the trial in protest at the change of judge.
"We want to say that the government is interfering in the trial. We cannot continue with our work fairly," lawyer Wudud Fawzi said.
"We want no interference with the trial from the government and we will not return until this condition is met."
A co-defendant, Ali Hassan al-Majid, the man dubbed Chemical Ali, also asked to leave the court.
But the judge ordered him to stay, to which Ali retorted that he would keep quiet "even if I am hanged."
Saddam and six of his colleagues face war crimes charges including genocide, for a military campaign against the Kurds in 1987-1988.
Prosecutors say 182,000 people were killed in the so called Anfal campaign in northern Iraq.
Saddam and his co-accused face the death penalty if found guilty.
Not the first time
The defence said the first chief judge in Saddam's previous trial over the killing of Shiite civilians in Dujail was forced to step down by the government.
Judge Rizkar Mohammed Amin cited "personal reasons" when he stepped down on January 23.
In that trial, Saddam and seven others were accused of killing 148 Shiites from the town of Dujail after an assassination attempt in 1982.
Human Rights Watch strongly also criticised the judge's removal, describing it as "a blatant violation of the independence of the court".
"This act jeopardises the integrity of the court and damages prospects of justice for the victims themselves," it said.
Government stands firm
Government spokesman Ali al-Dabbagh said "the decision to transfer the judge was taken to preserve the neutrality of the court."
Ameri came under fire from Kurdish and Shiite groups for telling Saddam he was "not a dictator."
His comments were made during a fiery exchange with the former strongman at a hearing on September 14.
Iraqi Kurds who were targeted in the Anfal attacks, welcomed Ameri's dismissal.
"Ameri was taking the court in a wrong direction," said Fuad Hussain, a senior official in the Kurdish regional government in northern Iraq.
Graphic tales of horror
Before adjourning to September 25, the court heard from five Kurdish witnesses.
They recounted how the people in their villages were gassed by Saddam's forces and imprisoned during the Anfal campaign.
Ahmed Qader described how after an attack on a nearby village, he and his brother collected dozens of gassed bodies and buried them.
"My eyes were watering and I was shaking (from the gas), but there was no other way to help," he said.
"Their eyes were popping out and their noses and mouths were bleeding."
Other Kurdish witnesses described their time in Iraqi prisons, including one woman who watched her niece and nephew die causing her to break down.
"A woman asked me what's the matter and I told her that my nephew and niece had died and she said that her own son had just died as well and we cried together until morning," said Shamsa Rustum.
She only found out about her husband's death when their identity cards turned up in a mass grave in 2005.
She then asked the court to return the two identity cards, which were being used as evidence, in memory of her lost husband.
"In my ID I'm wearing this necklace that my husband gave me," she pleaded with the court. "Can't you at least give me a copy?"
The prosecutor said he would try.