The judgment does not automatically reinstate the charges against Zuma, a decision that can only come from the prosecuting authorities.
Shaun Abrahams, head of the National Prosecuting Authority, told Reuters he was studying the ruling.
Opposition Democratic Alliance leader Mmusi Maimane, whose party brought the court application, demanded the charges against Zuma be reinstated.
"Jacob Zuma is not fit to be the president of this country," he told reporters.
"The decision that they took was irrational and we still maintain that Jacob Zuma is corrupt. Jacob Zuma must face the full might of the law. He has already violated the constitution. There is no debate about that."
The hundreds of corruption charges relate to a major government arms deal arranged in the late 1990s. Zuma said last week that an investigation into the deal had found no evidence of corruption or fraud