The polls have attracted 48 political parties with the leading contenders being the African National Congress, the Democratic Alliance and the Economic Freedom Fighters.
Analysts say the disillusionment with politics is a sign of growing unhappiness with the slumping economy and the proliferating corruption scandals, coupled with a lack of confidence in the two main opposition parties.
At time of writing the ANC, DA and EFF have the most votes with 54.71 percent, 26.41 percent and 7.98 percent of the counted votes respectively.
Most opinion surveys suggest the ANC will secure almost 60 percent of the vote, thanks to Ramaphosa's appeal and a fractured opposition. The election year before that - 2009 - the party won 66% of the vote.
Under South Africa's parliamentary system, the National Assembly chooses the country's president after the elections.
The ANC, which led the fight against apartheid, has governed the country since 1994.
Though the ANC will have a majority in parliament and Ramaphosa can expect the party to vote to confirm him in office with a five-year mandate, a better result would have helped the former labour activist turned tycoon in ongoing factional fighting within the party.
The white minority still owns disproportionately more land than the black majority.
In the most populous province, Gauteng, the IEC's Boitumelo Monaki said officials were responsive to concerns about possible fraud.
"As always in the election of this magnitude there are some challenges reported, including an instance where officials arrived late for duty and where materials were delayed".
The fringe party surprised many casual observers by surging into fourth place in early counts, eclipsing its one-percent take in the 2014 election, though its take remains in the single digits.
So, is South Africa about to see its first election in which national power changes hands? No. He was celebrating "that our country is now ruled by black people", he told the BBC.
Incumbent President Cyril Ramaphosa whose ruling ANC party has been in power since 1994 and is favourite to win despite corruption scandals, sluggish economic growth and record unemployment, was at Chiawelo Primary School in the Soweto district to perform his civic duty. "The party has done well especially after the doldrums we were in before the elections".
The fourth party is the Freedom Front Plus, with just about 4% of the vote. Matole voted ANC, telling Al Jazeera in a phone call that he was a "loyal citizen and loyal to his political party".
More than 40 smaller parties also took part in the election.
This has been a bad election for the DA which lost votes.
The party is reportedly banking on "Ramaphoria", voters' loyalty to Ramaphosa, despite senior leaders' skepticism of what his reforms could mean in practice.
The ANC's reputation was badly sullied under Zuma.
But the ANC faces widespread apathy among voters born after apartheid, known as the "born-free" generation, with millions who failed even to register to vote. "The ANC elected a leader who does not only talk about, but does practical things against corruption".