Judges Bhekisisa Mnguni, Thoba Poyo-Dlwati and Ester Steyn ruled against Zuma on Friday. He will now appear in the trial court on Tuesday, when he will face corruption charges.
Zuma's legal team relied on the National Prosecuting Authority's 15-year delay to prosecute and political interference to secure a permanent stay of prosecution.
Zuma's co-accused, French arms company Thales, also applied for a permanent stay of prosecution.
Thales is accused of agreeing to pay Zuma a yearly R500,000 bribe for protection from an investigation into the controversial multibillion-rand arms deal.
The alleged bribe was facilitated by Zuma's former financial adviser‚ Schabir Shaik.
