The Center for World University Rankings (CWUR) has ranked Wits University's as South Africa's best tertiary institution, with UCT coming in second.
But South Africa's universities did not enjoy global prestige with Wits ranking 176th in the world and UCT 265th.
Wits plunged 27 places from 149th place in 2015 to 176th this year. UCT dropped from 248th to 265th.
Stellenbosch was ranked number three in SA, but only 329th in the world - a drop of 23 places from 2015's 306th. UKZN came in fourth in SA but 467th in the world while the University of Pretoria was fifth in SA but 697th in the world.
CWUR publishes an annual ranking of universities according to the quality of education offered and the prestige which its faculty members enjoyed, including the quality of research produced.
Harvard was ranked first in the world and Stanford second with MIT coming in third.