Zuma had lodged a challenge at the court in Bloemfontein after a lower court decided in 2016 to reinstate the charges that were previously discontinued by prosecutors.
“The reasons for discontinuing the prosecution given do not bear scrutiny,” said Supreme Court judge Eric Leach who read the ruling.
The opposition Democratic Alliance party had sought in 12 court appearances since 2009 to reactivate the charges over controversial post-apartheid military contracts which have dogged Zuma for much of his time in government.
Zuma and other government officials were accused of taking kickbacks from the $5 billion purchase of fighter jets, patrol boats and other arms manufactured by five European firms, including British military equipment maker BAE Systems and French company Thales.
Charges were first brought against Zuma in 2005 but dropped by prosecutors in 2009.
In his reaction to the ruling, Zuma said he was “disappointed” by a Supreme Court of Appeal decision to uphold a High Court ruling to reinstate 783 corruption charges filed against him before he became president.
In a statement from his office, Zuma said he now expects the National Prosecuting Authority (NPA) to consider representations on the case before making decision to prosecute him.
State prosecutors set aside the charges in April 2009, paving the way for Zuma, who has faced and denied numerous corruption allegations made since then, to run for president later that year.
Zuma and the National Prosecuting Authority (NPA) were appealing against the High Court ruling, made in April 2016.
In his decision to reject their appeal, Judge Lorimer Leach said it was “irrational” for the NPA to have set the charges aside.
The NPA has responsibility for deciding whether to reinstate the charges, which relate to a 30 billion rand (2 billion dollars) government arms deal arranged in the late 1990s.
It was unclear when such a decision might be taken or if Zuma would approach the Constitutional Court to try to set aside the Supreme Court’s ruling.
The NPA would need to consider the judgment, spokesman Luvuyo Mfaku said, adding it would “at all times do the right thing within the confines of the rule of law and in the interest of proper administration of justice.”
The rand extended gains against the dollar after the Supreme Court’s ruling, which was unanimous.
“It is difficult to understand why the present regime at the NPA considered that the decision to terminate the prosecution could be defended,” Judge Leach said.