The Academic Ranking of World Universities (ARWU), released by Shanghai Ranking Consultancy, has been recognised as the most trustworthy of global university rankings.
Ranking for the best universities in the world is based on indicators, such as the number of alumni and staff winning Nobel Prizes and Fields Medals, the number of highly cited researchers, number of articles published in journals of nature and science, the number of articles indexed in science citation index and per-capita performance.
Harvard and Stanford in the USA fill the top two spots, while Cambridge in the UK took the third place.
Harvard tops the ranking for the 16th year.
Wits University has emerged as South Africa's leading university. It was ranked in the 201-300 category.
Wits scored 10% on the quality of education, 20% on the quality of faculty, 20% in the highly cited researchers divisio in 21 broad subject categories and 20% in terms of research output papers published in nature and science.
Other South African institutions that made the list include the universities of Cape Town, Stellenbosch and Pretoria.
The universities of KwaZulu-Natal and Johannesburg dropped off the list completely, while the University of Pretoria progressed into the top 500.
The other universities filling out the top 10 are the Massachusetts Institute of Technology, University of California – Berkeley, Princeton, Oxford, Columbia, California Institute of Technology and Chicago.