UCT retained its top title, with the University of Stellenbosch second, followed by Wits.
The report was released on Thursday by the 2018 Quacquarelli Symonds World University Rankings, which are released annually.
More than 70 000 academics and 30 000 employers contribute to the report.
The results included nine South African universities on its African list of 18 higher education institutions.
Worldwide, UKZN, which ranked in the 651-700 category last year, has dropped to the 701-750 category this year.
UCT also remains within the top 200 universities in the world at number 191.
Ranking is based on six categories - academic reputation, employer reputation, citations per faculty, student to faculty ratio, international faculty and international students.
Academic reputation is measured using a global survey in which academics were asked to identify the institutions where they believe the best work is taking place within their field of expertise and remains the biggest contributor to scores, making up 40%.
Three other African universities were included in the top 400 category - Stellenbosch at 361, the University of the Witwatersrand at 364 and The American University in Cairo at 395.
Others include the University of Pretoria (501-550); Rhodes; Northwest University and University of Western Cape (801-1000).
Meanwhile, in a separate ranking known as the Centre for Science and Technology Studies (CWTS) Leiden Ranking released earlier this year, UKZN was placed third in Africa and was ranked 436th in the world.
This ranking included 902 universities from 54 different countries worldwide and offers key insights into the scientific performance of major universities across the globe.
A sophisticated set of bibliometric indicators provides statistics on the scientific impact of universities and on universities’ involvement in scientific collaboration.
UKZN spokesperson Normah Zondo said the higher education institution was proud to have made the list.
“It is an achievement in itself to be included in the rankings as it indicates the approximately top 5% of the universities globally. A number of South African universities have fallen in position in recent years and this could largely be attributed to the negative perception formed out of the #FeesMustFall student protest action.”