The winning scheme ( pictured above and below) was chosen ahead of proposals by big-name architects including Britain's Allies and Morrison ( pictured bottom) which was pipped into second place.
Among the other stars to lose out on the $360 million (£200 million) campus project in Abuja, Nigeria, were Rafael Viñoly, Rem Koolhaas' Office for Metropolitan Architecture, Dutch practice SeARCH and Canadians Saucier + Perrotte Architectes.
The Nigerian 'centre of excellence' will become the inaugural project in a wider sub-Saharan scheme backed by the Nelson Mandela Institute (NMI), aimed at encouraging students to stay in Africa.
The Fuksas proposals include plans to carve one of Mandela's famous quotes into stone paving in the central Nelson Mandela square - a water-landscaped open space at the heart of the campus.
Judge Karl Voltaire, the chief executive of the NMI, said: 'The process allowed the AIST to be physically conceived by six of the world's best architects. It permitted us the luxury of being able to choose from these six.
'Two in particular stood out - that designed by Fuksas, of course, but also the design of Allies and Morrison.
He concluded: 'After extensive discussions with both, Fuksas was deemed to have the edge, but it was a difficult choice.'
Organised by the RIBA, the contest originally attracted more than 30 entries ( Allies and Morrison joins superstars on African shortlist
) and each of the shortlisted teams received an honorarium of $20,000 (£11,000).
Fuksas wins African science institute competition - images