A lawyer representing Aziz said the four-hour questioning session on Tuesday focused on the 1987-88 Anfal campaign - a depopulation scheme in which hundreds of thousands of Kurds were allegedly killed or expelled from northern Iraq on Saddam's orders.
Aziz also formerly foreign minister, has been in detention since he surrendered to US forces in April 2003.
"He denied all the charges and he was very calm and told them that there were no evidence for these accusations," lawyer Badee Izzat Aref said, breaking a gag order he signed earlier with the Iraqi Special Tribunal, calling it an "illegal request".
He said he would take his grievances to the tribunal's chief investigating judge, Raed Juhi, Iraq's chief judge, and to "public opinion and to humanitarian organisations".
"As long as the trial is not a secret one, I demand them to lift this illegal [gag] request," Aref said.
Aziz, 69, referred to Saddam as "president" and "leader Saddam Hussein" during his testimony, Aref said, adding that the panel also called in Saddam's former vice-president, Taha Yasin Ramadan, moments before Aziz entered.
Tariq Aziz called Saddam Hussein
president during the questioning
But he refused to answer questions because his lawyer was not present, Aref said
The pre-trial hearing took place at a US military detention complex near Baghdad airport where Aziz is jailed under US custody, Aref said. He said he spoke with his client over tea beforehand and brought him cigarettes.
"For the first time, US troops gave Aziz permission to take them," he said.
Only cabinet Christian
Aziz, the only Christian in the top Baath Party leadership, was allegedly involved in several party purges in the 1970s and 80s during which an unspecified number of people died.
He is at least the fourth person, including Saddam himself, to provide testimony in recent weeks to the Iraqi Special Tribunal investigating alleged war crimes during the government's time in power.
In Belgium, Iraq's Justice Minister Abdel Hussein Shandal accused the United States of trying to delay Iraqi efforts to interrogate Saddam, saying "it seems there are lots of secrets they want to hide".
But he also said he was confident investigators would wrap up the case against Saddam by the end of the year, underlining the Iraqi government's determination to try the ousted leader soon.