The decision to charge Zuma, who faces 16 charges of fraud, corruption and racketeering relating to 783 cases during an arms acquisition 20 years ago, was announced by Director of Public Prosecutions Shaun Abrahams who had previously protected Zuma from prosecution.
Last year a court ruled against a 2009 decision by prosecutors to drop the corruption charges against Zuma just months before he became president, laying the path to Friday's announcement.
State prosecutors previously justified dropping the case by saying that tapped phone calls between officials in then-president Thabo Mbeki's administration showed undue interference.
Zuma's criminal charges relate to an arms procurement deals struck by the government in the late 1990s and from which he is accused of profiting corruptly to the tune of four million rand (280,000 euros).
Zuma is accused of taking kickbacks from the four-billion-euro purchase of fighter jets, patrol boats and other arms, manufactured by five European firms, including British military equipment maker BAE Systems and French company Thales.
National Prosecuting Authority (NPA) spokesman Luvuyo Mfaku confirmed to the AFP news agency that Thales would also face prosecution, alongside Zuma.
Thales declined to make any immediate comment.
No timeline has been set out as yet for the legal proceedings, RFI correspondent Jean Jacques Cornish in Pretoria said, but the former president could appeal the ruling on a number of grounds and argue that the decision is illegitimate.
Zuma resigned as president last month after the ruling African National Congress (ANC) party threatened to remove him from office.
His successor, Cyril Ramaphosa, has vowed to tackle corruption, admitting it was a major problem in the previous government.