“The by-elections went extremely well today and the voting stations closed at 9pm,” said IEC spokeswoman Kate Bapela.
“We have not had any report that is worrisome. We believe the by-elections happened without much incident.”
Bapela said the counting process would begin after IEC officials took a break.
They would sort out the ballot papers in terms of political parties and then count and tally the ballots.
She said results would be posted on the website after they were audited, clarified and confirmed.
“The results are expected after midnight and normally by 10am tomorrow all the results would be finalised,” said Bapela.
“We hope communities made use of this opportunity to choose leaders locally.”
Municipal by-elections were held in nine wards across five provinces on Wednesday.
The positions became vacant after five councillors resigned and four died.
Four of the councillors who resigned were members of the Democratic Alliance and one was from the Congress of the People. All four of the councillors who died were ANC members, the IEC said in a statement on Tuesday.
In the Eastern Cape, three wards would be contested.
Ward four in the Buffalo City Metropolitan municipality in East London had 8515 registered voters. It was previously represented by the DA.
Ward one of the Nelson Mandela Bay Municipality in Port Elizabeth had 12,188 registered voters and was previously represented by a DA councillor.
Ward 56 of the same municipality had 11,978 registered voters and was previously represented by an ANC councillor.
By-elections would be held in two wards in the Free State.
Ward 20 in the Maluti-a-Phofung municipality, Qwa-Qwa, was previously represented by an ANC councillor. It had 4400 registered voters.
Ward 13 in the Ngwathe municipality, Parys, was previously represented by a DA councillor. It had 3586 registered voters.
In Limpopo a by-election would be held in Ward 10 of the Makhuduthamaga municipality, Ngwaritsi. The ward, previously held by a Cope councillor, had 4120 registered voters.
Mpumalanga would hold a by-election in Ward 15 of the Steve Tshwete municipality in Middelburg. The ward had 4607 registered voters and was previously represented by the DA.
The North West would hold two by-elections, in wards 13 and 15 of the Mahikeng municipality. Both were run by the ANC. Ward 13 had 5233 registered voters and the other 3799.