It is the latest blow to a powerful politician once seen as favourite to succeed President Thabo Mbeki in 2009.
“We have decided to bring criminal charges,” a national prosecuting authority spokesman said.
The director of public prosecutions, Vusi Pikoli, told Mr Zuma on Monday of the charges which include two counts of corruption.
Schabir Shaik, a friend of Mr Zuma from the anti-apartheid struggle and later his financial adviser, was convicted earlier this month of fraud and corruption and sentenced to 15 years in jail.
The judge found he and Mr Zuma had a “generally corrupt” relationship.
Mr Zuma’s sacking as deputy president was widely hailed as proof of President Mbeki’s determination to set an example for the rest of Africa by fighting official corruption, a vexing topic for international donors, lenders and companies.
But it has split the ruling African National Congress (ANC), where Mr Zuma remains party deputy president with a large following among the rank and file.
Mr Zuma, who has denied wrongdoing and hinted at a political conspiracy, said he was glad finally to have his day in court.
“I welcome this decision as it affords me an opportunity to respond to and clarify the allegations that have been made against me,” he said in a statement, adding he had asked the ANC to free him of party duties while staying as deputy president.
Mr Shaik was found guilty of soliciting an annual 500,000 rand ($A100,000) bribe for Mr Zuma from a French arms firm in return for protecting it from a probe into a massive arms deal.
He was also convicted of paying Mr Zuma 1.3 million rand ($A250,000) in bribes to encourage him to use his political influence to further Mr Shaik’s business interests.
The public prosecutor said in 2003 there was prima facie evidence against Mr Zuma, but a court case would be unwinnable — prompting angry rebuttals from Mr Zuma that he was being subjected to a politically motivated “trial by media.”