Mr Zuma said he disagreed with the way his party, the ANC, had pushed him towards the decision after the election of Cyril Ramaphosa as party president in December, but added, he would accept its orders.
His resignation came just hours after police raided the luxury home of the Gupta family, Indian-born billionaire allies of the president who have been at the centre of corruption allegations against Zuma and his circle for years.
All parties have always denied wrongdoing.
Jacob Zuma was ordered by the ANC, to step down as president on Tuesday.
When he didn’t the party announced that it would back an opposition motion in parliament to force him out.