The termination of the Zimbabwe Exemption Permit programme is for the benefit of the permit holders themselves, according to the Home Affairs Department.
The government will terminate the permits at the end of June, affecting roughly 180,000 Zimbabweans living in South Africa.
Under the original agreement, permit holders are not eligible for any other type of visa, including work, scarce skills or permanent residency.
Home Affairs Minister Aaron Motsoaledi says this means many of them are perpetually trapped in a temporary system with no means to better their lives.
"I don't think it's fair, even for us South Africans, to want people to remain temporary forever when their lives are moving."
He adds the department is assisting many permit holders to apply for new visas.
– Enca