The appointment, made on January 18, came after the government had set up afresh a search-cum-selection committee last September for shortlisting a candidate for the post, sources said.
The contenders for the top post included India's chief statistician T C A Anant and Tata Institute of Social Sciences chief S Parasuraman, they said.
The chairman's post remained ever since S Thorat's retired in February 2011. Since then Prakash had been the acting chairman of UGC.
The first search-cum-selection committee set up had shortlisted the name of director of IIM Bangalore Pankaj Chandra and former vice chancellor of Hyderabad University Sayed Hasnain.
However, their selection was marred by controversy prompting the government to start the selection process afresh.
Prakash has earlier served as Vice-Chairman and secretary of UGC as well as vice chancellor of National University of Educational Planning and Administration. He has also served as adviser Education in Planning Commission among others.