About 25 million registered voters - roughly half the population - began trickling into some 22,263 polling centres across the country from before dawn to exercise their right to vote in the fifth all-race elections.
Under the proportional representation system, South Africans are voting for parties, not candidates, in two simultaneous ballots for national and provincial governments.
Police said at least one officer will be on duty at every polling station and troops have also been deployed to keep order at various hotspots.
In some other areas, protesters threatened to disrupt polling over lack of service delivery.
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Except Western Cape Province where the main opposition party Democratic Alliance is in power, the ANC governs the other eight provinces.
The ANC is expected to win more than 60 per cent of the vote, even as its campaign has been hit by concern over economic problems such as high unemployment and a number of corruption scandals, analysts said.
After casting his vote, 72-year-old Zuma urged all citizens to come out and cast their votes without directly calling on them to vote for his party.
"This is our right that we fought for. Among the rights that we have, this is the most important right - to vote for your government," Zuma said.
But his deputy Cyril Ramaphosa, expected to succeed Zuma in the next elections in five years' time, was more forthright as he cast his vote in Soweto, calling on voters to make their marks for the ANC.