Shortly after Rice started speaking, three protesters stood up wearing black robes and black hoods, with their arms outstretched at their sides, an apparent reference to US abuse of detainees at Iraq's Abu Ghraib prison.
The crowd applauded as the protesters, shouting their opposition to the war in Iraq, were taken from the hall.
Rice seemed undisturbed by the interruption.
"In Baghdad, Kabul and soon in Beirut, they too will be able to speak their minds," she said.
About a hundred protesters demonstrated outside Davies Symphony Hall where Rice spoke during a long weekend trip to San Francisco
On Iraq, Rice said that country's democracy "is not going to look like the United States of America, but it's not going to look like Saddam's Iraq. And thank God for that, because it was time to get that monster out of the centre of Baghdad."
She acknowledged that Iraq's fledging democratic government had difficulties and that it was not unusual for historical changes to result in violence.
But she added that to date, the Baghdad leadership had not made a compromise "as bad as the one in 1789 that made my ancestors three-fifths of a man, so let's be humble about what they're going through".
"[Iraq] is not going to look like the United States of America, but it's not going to look like Saddam's Iraq. And thank God for that, because it was time to get that monster out of the centre of Baghdad"
US secretary of state
Rice was referring to a constitutional compromise in which three-fifths of a state's slaves were counted in deciding the state's representation in Congress and other issues.
Asked about the prospects for withdrawal of American troops from Iraq, she said President Bush thought that step could be taken only after success had been achieved.
"It would not be a good thing to leave before this job is finished," she said.