Earlier, Mr Zuma's governing ANC party told him to resign or face a vote of no confidence in parliament on Thursday.
The 75-year-old has been under increasing pressure to give way to Deputy President Cyril Ramaphosa, the ANC's new leader.
Mr Zuma, who has been in power since 2009, faces numerous allegations of corruption.
His resignation came at the end of a long speech in which he said he disagreed with the way the ANC had acted towards him.
He said he did not fear a motion of no-confidence, adding: "I have served the people of South Africa to the best of my ability."
The ANC issued a statement saying Mr Zuma's resignation provided "certainty to the people of South Africa".
Mr Zuma, a former member of the ANC's military wing in the days of apartheid, rose through the ranks of the party to become president. He led the country for more than a third of its time after apartheid.
But he leaves office with several scandals hanging over him, and with South Africa's economy in dire straits.
Source: SDK