On Friday, Judge Mnguni dismissed an application by Zuma and his co-accused, French arms dealer Thales, to have the charges set aside permanently with costs.
The 77-year-old politician was ousted last year after nearly a decade in power, following a bitter internal battle within the ruling African National Congress party.
Zuma's lawyers said the case is politically motivated and the years of delay will result in an unfair trial.
"Zuma has said for a long time that he wants to have the opportunity appear in court, but at the same he also tried to delay his appearance".
The country's High Court unanimously dismissed Zuma's bid for a permanent stay of prosecution over 16 counts of fraud, racketeering and money laundering relating to a multi-billion-dollar arms deal dating back to before he took office in 2009.
The case has been much delayed - the charges were first brought against Zuma in 2005.
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The judges blamed both Zuma and the state for the "systemic" delays, saying that "both parties are equally liable as they both participated in the litigation leading to the delay". Political analyst Xolani Dube warned that Zuma could lodge an "urgent" appeal.
Zuma is also set to continue is testimony before the Zondo commission either on October 21 to 25 just a week after his criminal trial or on November 11 to 15.
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 Treasury announced on Thursday that it was placing the Guptas under wide-ranging sanctions for their role in "a significant corruption network in South Africa that leveraged overpayments on government contracts, bribery and other corrupt acts to fund political contributions and influence government actions".