The prosecutor's office said Friday it would fight to make sure that taxpayers would not have to carry Zuma's legal costs in a forthcoming trial.
The charges relate to a R30-billion government arms deal in the late 1990s.
He successfully resurrected his bid for the presidency after the chief prosecutor dropped the charges against him in 2009, accusing his own officials of political interference.
Zuma also faces charges of racketeering, fraud and money laundering.
Abrahams said in his submission to the NPA that Zuma strongly disputed the allegations against him, insisting that he "lacked the requisite intention to commit any crimes listed in the indictment".
He will face 16 charges relating to 783 instances of alleged wrongdoing, National Prosecuting Authority spokesman Luvuyo Mfaku said.
He dismissed representations made by Zuma asking that the charges be dropped.More news: Pakistan ranked happiest among neighbouring countries
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When announcing his decision‚ Abrahams described the case as "long‚ litigious and unending".
In 2016, Zuma said a four-year investigation he set up while president had found no evidence of widespread bribery, corruption or fraud in the selection of bidders to supply the arms.
"It is a fight that we have been waging in the Courts for nearly nine years and today's decision is a vindication of the decision to challenge the dropping of the charges". In 2016, South Africa's High Court judged that the chief prosecutor's decision to set aside the charges was "irrational" - a ruling that was upheld by the Supreme Court a year ago.
Additionally, a judicial panel is preparing to view allegations of corruption at high levels of the South African government during Zuma's years in office. Shaikh was later released on medical parole.
There was no immediate comment from Zuma and it was not immediately clear when the former leader might go to trial.
Zuma, 75, resigned as president last month after he was ordered to do so by his party, the African National Congress.
"He must have his day in court..." Zuma insists he is innocent.