Many people joined the queues in the early hours of Friday morning in the hope of getting a permit South Africa has relaxed requirements for Zimbabweans to get permits to stay in the country, prompting thousands to queue at government offices.
They have to get correct paperwork before a new year deadline, otherwise they will face deportation.
Officials now say that passports are no longer required and those still in the queues by closing time will be seen.
Some two million Zimbabweans are estimated to be in South Africa, many of them illegally.
They have been fleeing recent instability and economic crisis in their own country.
In September, Zimbabweans working illegally in South Africa were told they had an opportunity to be processed and, if successful, given work visas and residency to stay.
So far, nearly 150,000 people have taken advantage of the amnesty and applied across South Africa in what correspondents say has been a painfully slow bureaucratic process.
Applicants have had to present their Zimbabwean passports, their birth certificates and letters from their employers or affidavits from the police to prove self-employment.
But many of the migrants crossed into South Africa from Zimbabwe illegally - without passports.
On Friday morning, Mkhuseli Apleni, director general of the Home Affairs Department, said this requirement had been dropped to encourage more people to apply and speed up the registrations.
He also said all those in the queues would be seen even after the offices closed at 1700 local time.
The BBC's Nomsa Maseko in Johannesburg says that, given the length of the queues, the process could last well into the night.
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