With barely hours to go before the cut-off, only 250633 Zimbabweans had applied to home affairs to legalise their stay, sparking fears of mass deportations of those who had failed to apply in time.
However, home affairs spokesman Ronnie Mamoepa, would not comment on when deportations would start, saying they were "focusing on mobilising people to regularise their stay in South Africa".
But Zimbabweans such as Roselyn Sithole are determined to avoid the humiliation of being herded into police vans and deported.
Despite being booted out of the long queue that snaked around the block at the home affairs offices in Harrison Street, Johannesburg, on Thursday morning, the heavily pregnant woman was determined to remain there until her application to legalise her stay in the country had been completed.
Sithole, 28, who is expecting her first child in a month’s time, had been waiting in the queue since 5am after walking two kilometres from her tiny apartment in Braamfontein.
Around 9am the hairdresser was ordered to move to the back of the queue by an unsympathetic policeman who thought she had jumped the queue.
Despite her aching and swollen legs, she took her place at the back and bided her time.
Ironically, home affairs officials and policemen stationed at the gates of the offices told the Sunday Times that preference to be at the head of the queue was given to pregnant women.
"If I go to the cops, they will embarrass me in front of the others," said Sithole.
She pointed to a policeman, saying: "He embarrassed me. He pushed me around."
She added: "I don’t want to be deported like an animal. That’s why I am here."
She expressed the hope that the deadline for applications for work, business and study permits would be extended.
"As you can see, we are too many here."
Later in the day, as the rain pelted down, Sithole, who had come armed with an umbrella, was still several hundred metres from the entrance.
Up until December 21 last year, home affairs had received 127564 applications for permits.
Another Zimbabwean waiting patiently in the queue, Patricia Vundhla, 43, a domestic worker living in Doornfontein, had been to the Harrison Street offices on three days this week in the hope of completing her application for a permit.
Although home affairs had relaxed the requirements for applying for permits, she, like many of her compatriots, was not aware of the changes.
"My employer, for whom I have been working for seven years, has refused to give me a letter confirming I am employed by her," she said.
This was one of the requirements that were relaxed by home affairs.
As the Sunday Times listened to her story, a warrant officer shoved and pushed a group of queue-jumpers, hitting one of them with his baton.
Scenes of chaos at the Zimbabwean consulate in Edenvale earlier this week, where queues were as long as 7km, had quiet-ened down by Thursday afternoon.
Themba Twala, 26, a waiter formerly from Bulawayo, arrived at the consulate at midnight on Wednesday to apply for his passport.
He had hoped to be first in the queue on Thursday morning, but ended up being number 50.
Twala, whose family live in the UK, said it was his dream to return to Zimbabwe one day, but he would go back only once circumstances had changed.
"I am tired. I just want to go home and sleep," he said, barely two hours before he was due back at work.
The long queues, however, provided ample business opportunities for taxi drivers and vendors stationed outside the Zimbabwean consulate.
Among those who made a killing was Zimbabwean-born Emmanuel Mabeza, an auto-electrician.
Mabeza was selling between 80 and 100 plates of pap and steak daily at R25 each.
"We are not taking advantage of the situation or exploiting the people. It’s just a good business opportunity," he said.
Other vendors were selling a plate of food for between R30 and R35.
Taxi drivers were charging passengers R8 a trip between Edenvale and the Johannesburg CBD.
Mamoepa said: "We are happy at the large numbers of people who have turned up at our offices in an attempt to regularise their stay." -Sunday Times