"When the deadline looms more and more people come out," departmental spokesperson Ronnie Mamoepa said.
"We welcome the large number of people who have come out."
He said that the process was running as planned.
Final figures of how many people applied would be available on Friday, he said.
Illegal Zimbabweans were given a deadline until 31 December 2010 to apply for documents to legalise their stay in their country.
Home Affairs offices across the country have been open between 08:00 and 17:00 in the days leading up to the deadline.
In April last year Pretoria announced a moratorium on the deportation of Zimbabweans and granted them a special dispensation for one year so that they could get documents from Zimbabwean officials based in South Africa.
The dispensation was to allow them to normalise their stay in South Africa.
Meanwhile, the Movement for Democratic Change said that the processing of passport applications came to an apparent standstill at the Zimbabwe Consulate at Beula Park, Isando, east of Johannesburg, on Tuesday.
"Nearly 50 000 Zimbabweans turned up," said MDC spokesperson Sibanengi Dube.
One of the documents Zimbabweans can use to apply for a legal stay in South Africa is a receipt showing that they have applied for a Zimbabwean passport.
Dube said security sealed off the entrance to the consulate on Tuesday.
He said some consulate employees apparently provided bank deposit slips to applicants in queues to pay money into government accounts to get service.
However, by late afternoon, bank slips ran out and the consulate started distributing SA Home Affairs application forms for work, study and business permits.
"Some applicants filled in their work permit forms and surrendered them to Zimbabwe Consulate offices, oblivious of the fact that the papers were supposed to be handed to South African authorities."