Counting began in each voting station shortly after polls closed, in some cities long after the planned 9:00 pm (1900 GMT) Wednesday shutdown, with long queues of voters snaking into the night.
With just over 10 per cent of votes tallied, the ANC was leading but with a score of 42 per cent -- well down on the 57 per cent it won in 2019 -- followed by the liberal Democratic Alliance (DA) at 26 per cent, according to electoral authorities.
The leftist Economic Freedom Fighters (EFF) was in third place with eight per cent of the vote, trailed by former president Jacob Zuma's uMkhonto weSizwe (MK) with seven per cent.
The final results are not expected to be known before the weekend.
If President Cyril Ramaphosa's party is confirmed as dropping below 50 per cent for the first time since it came to power in 1994 -- in South Africa's first democratic, post-apartheid election -- it would force him to seek coalition partners if he is to be re-elected to form a new government.
That would be a historic evolution in the country's democratic journey, which was underlined by newspaper headlines on Thursday.
"SA on the cusp of a shift in politics," read the front page of daily BusinessDay.
"The people have spoken" headlined The Citizen, adding that the long queues were "reminiscent" of those that brought late liberation leader Nelson Mandela to power three decades ago.
The Independent Electoral Commission (IEC) said a last-minute rush in urban voting and high turnout were to blame for Wednesday's late finish and predicted the final turnout would be "well beyond" the 66 percent recorded in 2019.
However, many voters complained at polling stations that the three-ballot system was too complex.
IEC general manager of electoral operations Granville Abrahams said that "under the circumstances", electoral authorities "could have done better".
