He maintained the case was politically-motivated and years of delay would result in an unfair trial. Both the French firm and the former president deny any wrongdoing.
The defence also argued that there was vast political interference in the matter which met his client could not be afforded a fair trial.
He also said Zuma's claims that he was a victim of a "witch hunt" were unfounded.
The charges date back to 2005 when the former president received 783 payments totalling over R4m from his then-financial adviser Schabir Shaik. Zuma, who was forced to resign previous year over multiple graft allegations, is alleged to have taken the bribes during his time as a provincial economy minister and later as deputy president of the ruling African National Congress (ANC) in the 1990s.
Zuma's co-accused French arms company Thales in their application for a permanent stay of prosecution also argued that there had been an unreasonable delay in the prosecution and the company being charged along with Zuma was a "knee-jerk reaction by the NPA" to just lump similar charges faced by Zuma on them.More news: Iranian women allowed to watch live football match
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"The family has been implicated in several corrupt schemes in South Africa, allegedly stealing hundreds of millions of dollars through illegal deals with the South African government, obfuscated by a shadowy network of shell companies and associates linked to the family", the statement said.
South Africa's main opposition party the Democratic Alliance welcomed the court's decision, saying "that Zuma will eventually have to face his day in court". Political analyst Xolani Dube warned that Zuma could lodge an "urgent" appeal.
His successor, President Cyril Ramaphosa, has vowed to crack down on the widespread graft that has eroded support for the ANC, which has ruled the country since the end of the harsh system of white minority rule known as apartheid in 1994.
The US Department of Treasury's Office of Foreign Assets Control (OFAC) announced on Thursday that it had issued wide-ranging sanctions against Atul, Rajesh, Ajay Gupta and their business associate Salim Essa.