Former president Jacob Zuma's application for a permanent stay of prosecution in relation to his fraud, money laundering, racketeering, and corruption charges has been dismissed with costs.
The ruling means further scrutiny of a 1999 arms deal in which Zuma is accused of receiving bribes from French arms manufacturer Thales.
Mr Zuma's legal team argued his court case had been prejudiced by long delays and there was political interference in his prosecution.
The 77-year-old has denied any wrongdoing and has said he is the victim of a politically motivated witch-hunt.
The NPA had the opportunity to prosecute Zuma alongside Shaik in 2004 but declined to do so, even though it said it had a prima facie case against Zuma.
State lawyer Wim Trengove had pushed for prosecution arguing that if Mr Zuma did not face trial it gave the impression that he had received special treatment "because he is an important and a powerful man".
They abandoned the case months before he became president in 2009, saying taped phone calls indicated that the chief investigator may have used the case to frustrate Zuma's efforts to win control of the ruling African National Congress.
The charges date back to 2005 when the former president received 783 payments totalling over R4m from his then-financial adviser Schabir Shaik.
"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.
The ANC party forced him to resign past year over a separate corruption scandal centred around the wealthy Gupta business family, who won lucrative contracts with state companies and allegedly held sway over his choice of cabinet ministers.
Zuma is also expected to have two appearances in October and November at the state capture inquiry.
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