The award, established in 1977 and in its 30th year, is run every three years and aims to encourage architecture which 'respects the traditions of Muslim societies'. Foster will split the $500,000 (£250,000) prize money with eight other awarded projects.
Norman Foster picked up the award in person from the Aga Khan at a ceremony in Kuala Lumpur, Malaysia.
In a citation, the Aga Khan said the university had 'attained the highest standards of architectural excellence while reflecting the values of its specific environment'. He also said the building was an 'inspiration for progressive education'.
The other awarded projects, whittled down from 342 entries, are: