The Independent Electoral Commission (IEC) said this was the first time it has faced allegations of multiple voting.
Several political parties have lodged complaints, while South Africans took to social media claiming they were able to cast ballots more than once.
Eyewitness News has seen videos of people able to vote more than once, easily breaching security measures at polling stations.
The commission held a briefing just before midnight, as social media went on overdrive about discrepancies in the disappearance of what is supposedly indelible ink and claims of multiple voting.
The IEC has confirmed it was investigating two cases of multiple voting brought to its attention.
Commissioner Mosotho Moepya admitted that they have never crossed this road before.
“We’ve never been here before, it’s possible that something has happened. We’re saying we’ll pursue every one of these instances.”
However, he said if evidence of electoral fraud was found, the results from those voting stations would be quarantined and suspected fraudsters prosecuted.
“They’d have left footprints with us and we’ll pursue those footprints.”
Despite the allegations, Moepya insisted the integrity of the sixth democratic elections was still intact.