Higher Education Deputy Minister Buti Manamela is encouraging students to use the Central Application Clearing House (CACH) instead of applying in person at universities.
"It was worrying that some prospective students would prefer that method over the CACH," the minister said.
"The central application is best suited to place students at universities," he added.
Manamela said those who haven't had a chance to enrol at a university to study further in 2019, still have a chance to do so if there is space.
Manamela visited the CACH's call centre on Tuesday morning to assess how it assisted prospective students with placements.
"It is an important platform for our students and universities to be able to ensure that we have successful registrations," said Manamela.
He urged universities to continue using the service, saying it would aid students to find courses which aren't full.
"We are quite excited that already in two weeks, we are almost matching the numbers for 2018 in terms of the use of the central application system."
At the same time, the National Student Financial Aid Scheme has rejected 65 000 applicants, and granted funds to just over 300 000.
The scheme's spokesperson, Kagisho Mamabolo, said 50 000 others did not submit supporting documents but could still do so on campus.
"NSFAS is now considering funding for late admission. The appeal will be opened," Mamabolo tweeted.
Scores of students who enrolled at different tertiary institutions flooded social media to voice their dissatisfaction with the scheme's application process.
Some claim their application for funding was rejected without reason, saying their parents or guardians were either unemployed, or did not earn enough to afford their fees.
The NSFAS was at the centre of widespread protests on campuses across the country in recent years, with students complaining about the non-payment of funding benefits.
Mamabolo said it at the time that rejections could be attributed to incorrect information or verification data from third-party credit agencies reflecting a different income.
The minister, however, has highlighted that beneficiaries of state grants "are not even subjected to a means test. They qualify automatically."
