The charges, relating to a multi-billion dollar arms deal, were dropped by the chief state prosecutor in a move that cleared the way for Zuma to be elected president.
"The decision... To discontinue the charges against Mr Zuma is irrational and should be reviewed," Pretoria High Court judge Aubrey Ledwaba said.
"Mr Zuma should face the charges as applied."
The prosecutor had justified dropping the charges by saying that tapped phone calls between senior officials in then-president Thabo Mbeki's administration showed political interference in the case.
DA leader Mmusi Maimane said Friday's court ruling was a major blow for the president, who has faced months of criticism over various corruption scandals and the country's dire economic outlook.
"Today is a great victory for the rule of law. Ultimately Jacob Zuma must face prosecution," Maimane said after attending the court hearing.
"We are deeply, deeply delighted. We believe it's a significant judgement.
"Jacob Zuma must have... His day in court."
But the legal wrangling is set to continue, with the ruling likely to go to appeal.
The president last month lost another major legal case when the country's highest court found he violated the constitution over the use of public funds to upgrade his private residence.
The so-called "security upgrades", which cost taxpayers USD 24 million, included a swimming pool, chicken run, cattle enclosure and an amphitheatre.
The DA and other opposition parties attempted to impeach him in parliament, but the ruling African National Congress (ANC) used its majority to easily defeat the motion.
Pressure on the president to be ousted or to resign has grown with several veteran leaders of the party that brought Nelson Mandela to power in 1994 calling for him to step down.
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