Some polling stations ran out of ballot papers as millions of voters turned up to cast their votes despite the weather.
IEC chairperson Brigalia Bam said except for "a few glitches" the elections were peaceful.
She also said the elections were executed with the kind of efficiency expected from an institution that has successfully done so previously.
"There was no intimidation and there was no violence.
"All polling stations were operational in South Africa's fourth general election and everything was peaceful, tranquil and harmonious. Almost all the voters stations opened on time and were operating well," she said.
The "few glitches" Bam referred to included incidents of shortages of ballot boxes in areas such as Soweto and Centurion.
IEC chief electoral officer Pansy Tlakula said one reason for the shortages was that some ballot boxes were used for special voting on Monday and Tuesday, where unexpected numbers of voters who had not applied for special voting in time had turned up to vote.
Some of the bigger voting stations in Free State ran out completely and excess ballot papers from quieter stations had to be delivered.
The ANC's Jessie Duarte said yesterday the ANC hoped the IEC would extend voting hours.
Other parties also raised concerns about shortages, with the DA saying 24 polling stations in Gauteng, Western Cape and Free State had run out.
Tlakula said the IEC would decide later last night whether to extend voting hours.
Other reported incidents of disruptions included one in Kwazulu-Natal where a presiding officer was caught with ballot papers already marked with voting crosses for the IFP. The presiding officer was arrested and is to appear in court today.
In another incident, a presiding officer in Nkandla reported the disappearance of 50 ballot papers.
In Limpopo, a presiding officer was dismissed after he was found guilty of acting in a manner that favoured the ANC.
And in North West a presiding officer attempted suicide by stabbing himself with a pair of scissors.
Tlakula said presiding officers had undergone a security process before their appointment.
The elections have also received a thumbs-up from political analysts.
"South Africans bring a certain normality to elections which makes us really proud.
"In other countries people get killed during elections for holding a different political view," said analyst Xolela Mangcu.
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