- Professor Makgoba was the first recipient of the South African-German Science Award in the category of Top Researcher,“for having made outstanding extraordinary contribution(s) of international standard and impact to the development of science, in and for South Africa, over an extended period of time", 2012;
- Professor Makgoba was the recipient of The National Research Foundation President’s Life Time Achiever Award on 1st September 2011 “for having made outstanding extraordinary contribution(s) of international standard and impact to the development of science, in and for South Africa, over an extended period of time";
- Professor Makgoba was elected Vice-President for Planning and Review of the International Council for Science (ICSU), 30th September 2011;
- Recipient of the 2011 Le Matinel Educational Excellence Award for “Outstanding Contribution to Education”, 14th December 2011;
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