Zuma, who was president between 2009-2018, faces 18 charges relating to the 1999 deal. He has rejected the charges and says he is the victim of a politically motivated witch hunt by a rival faction of the ruling African National Congress.
Zuma, who also faces a separate inquiry into corruption during his time as president, is accused of accepting R500,000 annually from French arms company Thales, in exchange for protecting the company from an investigation into the deal.
"I plead not guilty," he said, staring into space, after the prosecutor read out all the charges.
Zuma's defence team is calling for the recusal of state prosecutor Billy Downer, on the grounds that he has "no title to prosecute". The prosecution requested more time to make a response to that call, so it will not be dealt with on Wednesday but rather on 19 July, said the presiding judge.
Thales was known as Thomson-CSF at the time of the deal. It has said it had no knowledge of any transgressions by any of its employees in relation to the award of the contracts. Its representative in court also pleaded not guilty to the racketeering, corruption and money laundering charges the company faced.
The National Prosecuting Authority filed the charges against Zuma more than a decade ago, set them aside just before he successfully ran for president in 2009, then reinstated them a month after he resigned in early 2018.
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