Aziz was the first defence witness in the trial which sees Saddam facing charges of crimes against humanity and possibly the death penalty if found guilty.
While he was not involved with the events of Dujail itself, his testimony on behalf of Saddam focused on the series of assassination attempts against officials of the Ba'ath regime at that time.
"The president is not guilty, nor are any of the officials in the government, just because they punished those who tried to assassinate the head of state," he told the court.
"The Dujail case is part of a chain of assassination operations against officials and I am one of the victims," he said.
Aziz, looking tired, asserted that current government officials should be in the dock instead of him, accusing one of the now ruling Shi'ite parties of having tried to kill him and Saddam in the 1980s.
"I was exposed to an assassination attempt by a political party," he told the court. "I am a victim of criminal acts by a party presently in power. Try them."
Aziz was number 43 on the US most wanted list of Iraqi officials when he gave himself up to US forces in April 2003 just two weeks after Saddam's government fell.
At the previous trial session on Monday, one of the former president's half-brothers gave testimony for Saddam's former intelligence chief.
All the eight defendants, including Saddam, were present when Wednesday's session got under way.
They are accused of bloody reprisals, including the killings of 148 men and teenagers, in the Shi'ite town of Dujail after a failed assassination bid on Saddam in 1982.
In 1980, Aziz was attacked by militants who tossed grenades at him at Baghdad's Mustansiriyah University.
"The president of the state in any country, if faced with an assassination attempt, should take procedures to punish those who conduct and help this operation," he said.
"According to the law, people who support this assassination can also be convicted."
The trial is currently in the defence phase, featuring testimony on the behalf of the accused, with last week involving witnesses for the little know Ba'athist officials from Dujail.
Up to 60 defence witnesses are lined up to testify, and prosecutors said the defence testimony could take weeks.
Proceedings could end by late June, with a verdict possible as early as July.
The trial, which opened on October 19, has been marred by repeated tirades from Saddam and other defendants, the murder of two defence lawyers and the January resignation of the first chief judge.
Lebanese lawyer Bushra Khalil returned to the courtroom after a long absence following her expulsion in early April by Judge Rauf Abdel Rahman for disrupting the proceedings, but was thrown out again almost immediately after an argument erupted.
Elsewhere in Baghdad, gunmen shot dead a Baghdad police general on his way to work on today, a city official said.
The killing of General Ahmed Dawod, a deputy chief of Baghdad municipality's protection units, appeared to be part of a campaign to assassinate prominent Iraqi officials.
It comes a day after three separate bomb attacks killed at least 21 people in the Iraqi capital on yesterday, including 11 people in a nearby sandwich shop when a bomb hidden in a motorcycle exploded outside a Shi'ite mosque.