Rauf Abd al-Rahman, the new chief judge in the case, told the defence team in opening remarks on Sunday he would not allow political statements.
"This court is not a place for political speeches," he said.
Within minutes of the trial resuming, Abd al-Rahman ejected Barzan al-Tikriti, Saddam's half-brother and former intelligence chief.
Al-Tikriti was dragged out by court guards after he refused to keep quiet and called the trial "a daughter of a whore".
The defence team protested that they were being treated unfairly and threatened to leave.
Abd al-Rahman told them: "If you leave, then you can't come back for future sessions."
Saddam's chief lawyer, Khalil al-Dulaimi, said the US-sponsored court was illegal and "run by the Americans".
He and his colleagues then left the courtroom.
When some of the defendants stood up to leave as well, Abd al-Rahman told security guards to sit them down.
"I want to leave," Saddam, dressed in a dark suit and collared shirt, told the judge.
"This court is not a place for political speeches"
Rauf Abd al-Rahman,
"Then leave," said Abd al-Rahman.
"It is a tragedy. I led you for 35 years. How can you lead me out of court?" Saddam asked.
"You wanted to leave," the judge replied shortly, after which Saddam left.
He was followed by his former vice-president, Taha Yasin Ramadan.
Order was later restored to the court, which began to hear a female witness, who testified from behind a curtain to protect her identity.
The trial resumed without the defence team, Saddam or any of the high-profile defendants present.
The court has been in turmoil since Kurdish chief judge Rizgar Amin resigned, complaining of pressure from the Shia-led government to speed up the process and crack down on Saddam and some of his co-accused, whose outbursts have
dominated proceedings thus far.
The trial has also been marred by numerous delays since getting under way last October.
Two members of the defence team have been murdered, and Amin's original replacement was accused last week of being a former member of Saddam's Baath party.
Sunday's trial resumed after
a series of delays
Sunday's session was the eighth since the trial began on 19 October.
It was due to have resumed last Tuesday but was postponed for five days.
The trial was adjourned until Wednesday or Thursday.
"The court is adjourned until Wednesday unless it is a holiday, in which case until Thursday, February 2," said Abd al-Rahman after three witnesses testified on Sunday.
The government has already declared Monday and Tuesday as holidays in Iraq to mark the new Islamic year.
The Islamic new year falls on either Monday or Tuesday and is marked by a public holiday.
Saddam and seven co-accused are on trial for crimes against humanity, charged with killing 148 men from the Shia town of Dujail after a failed attempt to assassinate Saddam there in 1982.