The system of higher education functions as a basic factor of progress in all social spheres, determining the prospects of the country’s economic development in the long run. Such a role of the higher education system becomes especially relevant in the transformation (transition) periods characterized by profound systemic changes, since exactly this specific sphere of social economy predetermines the quality of the intellectual capacity provided by generation of new (creative) knowledge functioning as the resource of transformational changes and outrunning transition to the innovational-intellectual development stage of the post-industrial era. The article may be of interest for scholars studying the innovation processes realized in the context of transformational changes of Russian economy with account of the leading role of higher school as a subject ensuring intensification of the intellectual capital reproduction.