It said the validation exercise was conducted independently by Statistics South Africa based on voting station result data from 1,020 voting stations.
Not all of them were new to election contestation but collectively, they could not secure more than 40,000 votes.
The governing African National Congress said it was impressed by the way the IEC handled the challenges it had faced.
The commission announced on Thursday that it had established an audit to probe the extent of voter fraud after political parties complained that the ink used on voters’ thumbs was easy to remove.
The IEC said by 10pm there should be a clear picture of which parties had done well in the national and provincial elections.
The commission met with angry party leaders on Thursday morning following allegations of voter fraud.
These issues, among others, were reported by observers monitoring the elections in Cape Town.
Among these areas is Umlazi township where residents were protesting on Mangosuthu Highway and barricaded roads.
IEC chairperson Glen Mashinini was reportedly unable to confirm if the ballot boxes belonged to the commission but the IEC has launched an investigation into the matter.
According to the IEC, 26.5 million voters are eligible to cast their votes at the polls on 8 May.
The 2.4 million registered voters, more than a quarter of whom will be casting their ballot for the first time, will have not fewer than 299 parties to choose from.
The youth have been the main target of political parties whose leaders will be crisscrossing the country in a bid to register first-time voters.
The IEC is encouraging young people who have not yet registered to do so this weekend and those who have registered before, to change their address online.
The new political party, which is registered with the commission, says it has written to President Cyril Ramaphosa asking that he get rid of foreigners.
Stephen Grootes says we shouldn’t be surprised when the ANC attacks other institutions of our democracy.
Vuma Mashinini believes he is the right man for the job as IEC chair, & will prove this.
Judith February looks at the thorny issue of independence and the position of IEC chair.
Parliament wants President Jacob Zuma to appoint Glen Mashinini to fill the commissioner's seat in IEC.
