"After due consideration for the facts in the relevant case docket, the National Prosecuting Authority (NPA) has decided that Jacob Zuma be arraigned in the Johannesburg Magistrate's court on a charge of rape," the prosecuting authority said in a statement on Tuesday.
"To this end Mr Zuma duly appeared in the Johannesburg Magistrate's Court today 6 December 2005 where the indictment and related documentation was served on him," the NPA said.
It said Zuma was freed on a 20,000 rand ($3140) bail and his case would be heard from 13 February next year.
Zuma on Tuesday denied rape charges against him and attacked the media for reporting the allegations, saying it had caused "great prejudice" to him.
"I wish to state clearly that I am innocent of these charges,"
said Zuma in a statement released by his lawyer after appearing before a Johannesburg court where he was formally charged with rape.
"I am deeply disturbed that what is purported to be evidence has been led in the media. This has severely influenced public opinion on this matter, causing great prejudice to me," he said.
Shabir Shaik, Zuma's financial
adviser, was convicted of fraud
Zuma is already facing a corruption trial stemming from the conviction for fraud of his former financial adviser.
Although he is popular among rank and file members of the ruling African National Congress (ANC), analysts say a rape charge against him looked certain to silence his followers who allege he is a victim of a political conspiracy.
The ANC had no immediate comment on Zuma's court appearance.
President Thabo Mbeki sacked Zuma in June after his deputy's former financial adviser Shabir Shaik was convicted of corruption and fraud in a court ruling that said the relationship between the two men was "generally corrupt".
Zuma as deputy president was in pole position to succeed Mbeki in 2009.
His rape charge could heat up the political temperature, as top ANC officials manoeuvre to position themselves for the top job.
He has rejected the charges of corrpution as a conspiracy to sideline him from the ANC leadership.
The rape allegations were first published by newspapers last month.