Faced with a massive election turnout, the Independent Electoral Commission decided on Wednesday night to keep polling stations around South Africa operating until the last person waiting in line had voted.

"All stations are closing at 9pm, however all voters who will be in the queue at the time will be allowed to vote," IEC commissioner Terry Tselane said in Pretoria.

The announcement followed party calls, led by the ANC, to extend voting hours past the deadline of 9pm on a election day marked by ballot shortages and snaking queues reminiscent of the first
democratic elections 15 years ago.

Tselane said presiding officers had "scrambled" to supply some stations suffering from shortages with voting material. The IEC however denied a statement by the Inkatha Freedom Party that mere hours before cut-off time, a million more ballot papers were being printed.

Polling stations came under intense pressure in Gauteng, with more than five million voters, and in the fiercely contested Western Cape, where the Democratic Alliance is hoping to snatch power from the ANC.

DA leader and premier candidate Helen Zille lambasted the IEC for running a chaotic election, and hinted that conditions would favour the ANC as it tries to retain a two-thirds majority.

"I think the turnout was great but the IEC was pathetic. They ran out of ballot papers, they ran out of ballot boxes," she said.

"You don't extend voting hours because you failed to get it right the first time round. It really makes me so angry.

"It will only benefit the ANC because they have queues going round the block."

The IEC blamed the problems on a last-minute concession allowing  voters to cast their ballots at the polling station of their choice.

"The shortage of ballot boxes and papers was caused mainly by the provision in the Electoral Act that allows voters to vote at voting stations other than the ones where they are registered," said Tselane.

"This also resulted in long queues."

The IEC also came under fire from the ANC's campaign manager Chris Nissen in the Western Cape, who said "very serious" problems at many voting stations in townships like Khayelitsha and Philippi saw voters trudging home without having cast their ballots.

"This matter has been repeatedly raised with the IEC over many months.

It appears the ANC's worst fears have been confirmed," he said.

In Soweto, tempers flared between IEC presiding officers at neighbouring polling stations as they ran out of provincial ballot papers.

Tshilidzi Primary School voting station presiding officer Hector  Muthabi told Sapa he was forced to redirect voters registered elsewhere to their proper voting districts, prompting a colleague from Gazankulu Primary School to shout at him for turning people away.

"She walked in and started accusing me of chasing voters away," he said.

Despite such incidents, and at least one case of suspected fraud, IEC chairwoman Brigalia Bam insisted that the commission had matters in hand and that voting had been smooth and peaceful.

"Everthing is tranquil, peaceful and harmonious, and the best news that we have received is no violence, no intimidation reported."

IEC chief electoral officer Pansy Tlakula refused to concede a shortage of ballot papers for the national elections, telling reporters at the commission's result centre in Pretoria: "I still do not know if that is fact or fiction.

"Nobody came to us and said that they ran out."

Tlakula did however admit to a shortage of official ballot boxes that forced the commission to procure plain cardboard ones.

She blamed the problem on the sheer size of ballot papers in the country's most competitive post-apartheid vote as 25 parties slugged it out with the ANC for a potential 23 million votes.

"Once you fold this ballot paper it is quite thick."

The IEC said counting would also get underway at each voting station "immediately" after 9pm.

Analyst Adam Habib said with the ANC cruising to victory for the fourth time, all eyes would be on the closely-fought race between the DA and the four-month-old Congress of the People for second
place.

"The real race here is for second place... and that race is going to be closely contested."

Habib said Cope had given opposition voters an alternative platform as the party had a "fundamentally different image" from that of the DA.

Former president Thabo Mbeki refused to say whether he had given his vote to the breakaway party formed in protest after he was ousted from his post by supporters of presidential frontrunner
Jacob Zuma.

"It is a secret ballot. Really, I think it is very important that people understand that, because the future of our country depends in part in people voting according to their consciences," Mbeki told reporters in Parktown, Johannesburg.