Eight defendants, including Aziz, are facing charges in the case.
One of the accused is Ali Hassan al-Majid, widely known as "Chemical Ali", who was not in court as he faces a pending death sentence in another case.
Merchants killed
The defendants are accused of involvement in the killing of 42 merchants who were accused of manipulating food supplies to drive up prices at a time when many Iraqis were suffering economically.
The merchants were rounded up over two days in July 1992 from Baghdad's wholesale markets and executed hours later after a quick trial.
Their bodies were returned to their families the following morning.
Relatives of the men deny allegations that they were manipulating prices.
Some believe that they were killed because their power to set prices during sanctions meant they posed a threat to the Saddam regime, Owen Fay, Al Jazeera's Baghdad correspondent, said.
Others say that members of the ruling Baath Party wanted to control the market and had the businessmen killed to remove any competition.
Execution orders
Critics say the present government is punishing Aziz for refusing to testify against Saddam Hussein, Iraq's former president.
"The Iraqi government also wants to avoid the public criticism for keeping an ailing man in prison for five years without presenting any charges against him," Aziz's son, Ziad, said in a telephone interview from Jordan.
Aziz, the only Christian among Saddam's mostly Sunni Muslim inner circle, was the public face of the Iraqi government during the first Gulf war and in the following years.
The judge said Aziz was being prosecuted because he signed the execution orders against the merchants as a member of Saddam's Revolutionary Command Council.
Aziz's lawyer has said the charges against his client are "baseless".
"There us no credible accusation against Aziz," Badia Arif, Aziz's lawyer told reporters.
"The prosecution assumes that just because he was a member of the Revolutionary Command Council, which carried out the death sentences, he is guilty," Arif said.
If convicted, Aziz, who was number 25 on the US most-wanted list after the Iraq invasion, and his co-defendants could face death by hanging.