"The conclusion of the court below that the decision to terminate the prosecution was irrational can not be faulted", judge Eric Leach said in his ruling delivered in Bloemfontein.
The High Court in Pretoria ruled earlier this year that the 2009 decision to withdraw charges was irrational and set it aside which had the automatic effect of the charges being reinstated against the president.
But he wanted the opportunity to make fresh representations before the NPA made a decision to recharge him.
NPA spokesman Luvuyo Mfaku, speaking to the SABC following the judgment, said NPA boss Shaun Abrahams and his leadership team would consider the judgment and interrogate it before commenting.
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Both the NPA and Zuma turned to the SCA after the High Court denied them direct access for an appeal.
The National Prosecuting Authority and Mr JG Zuma are to pay such costs jointly and severally, the one paying the other to be absolved.
SCA Justice Eric Leach upheld the High Court's view that the decision to withdraw 783 charges of corruption and fraud against Zuma was irrational. "It is hard to understand why the present regime at the NPA considered that the decision to terminate prosecution could be defended".
"That is then correct, yes", Kemp replied at the time.