With about 99 per cent of the results out, the African National Congress had won 62.2 per cent of the vote, down from 66 per cent in 2009 elections.
The Democratic Alliance, which is the main opposition group, got 22.2 per cent, up more than 5 per cent since the last election.
Julius Malema's populist Economic Freedom Fighters party bagged 6.25 per cent of the votes.
With a record number of 29 parties contesting the polls, opposition to the ANC was hugely fragmented, paving the way for 72-year-old Zuma to return to power, despite controversies including claims of corruption, unemployment and a sluggish economic growth during his first tenure.
He was dogged by allegations of corruption in the build-up to the election after an independent inquiry found he had "unduly benefited" from an expensive government-funded upgrade to his private residence.
Zuma, speaking while casting his vote on Wednesday, said he thought "the results will be very good", but added that the campaign had been "very challenging".
This will be ANC's fifth consecutive term but in this election the opposition had gained significant ground as compared to previous polls.
The Democratic Alliance has seen an increase in the number of black supporters, the party said today.
"Roughly 760,000 black South Africans voted for the DA," Zille told reporters.
South Africans have voted for parties, and not candidates, in a dual national and provincial ballot on a proportional representation system, with the winning parties deciding on the President and nine provincial premiers.
Those born after the end of apartheid in 1994 were able to cast their ballots for the first time with the turnout just over 72 per cent. A record 25 million voters were eligible to vote in the elections.
