Eight court-appointed lawyers stood in for the defence team, which stayed away in protest at the sacking last week by the Iraqi government of the previous chief judge.
The new judge had ejected Saddam during the last hearing on Wednesday, when the defence attorneys had also stormed out in anger.
During a noisy exchange on Monday while one of the six other defendants quizzed a Kurdish witness, Saddam waved a yellow paper from his seat in the metal pen where the defendants sit, saying it was a request to be allowed not to appear in court.
"It dishonours me to talk to you," he told the chief judge.
"And I don't want to be in this cage any more."
Telling him "It's not up to you" and scoffing at Saddam's claim to legal qualifications, judge Mohammed al-Ureybi said he failed to observe courtroom discipline and was banishing him from court.
"Take him out," he told the guards.
The case concerns the Anfal offensive by Iraqi forces in the Kurdish north in 1988.
"I don't want to be in this cage any more"
The court-appointed lawyers spoke up to interrogate witnesses from time to time.
One of Saddam's co-defendants complained he did not want to be represented by someone he did not recognise.
Another accepted an assurance from the judge that he would have a chance to meet his new attorney later.
The court was later adjourned till Tuesday after hearing three witnesses.
The trial is the second Saddam has faced. A verdict in a year-old trial for crimes against humanity over the killing of 148 Shia is expected next month. The first chief judge in that trial quit in protest against political interference.