With continuous growth of students' enrolments in the public universities and limited funding, assessing the efficiency of universities is vital for effective allocation and utilisation of educational resources. Are higher education institutions in South Africa making the most efficient use of resources made available to them? This study attempts to provide an answer to this question. We apply a Data Envelopment Analysis (DEA) method to estimate technical efficiency (TE) of 22 public universities in South Africa for the period 2009 to 2013. A university is said to be efficient if it is producing maximum output (number of graduates and publications) from a minimum quantity of inputs (staff numbers, students' enrolments, and expenditure). The results indicate that over the study period the average TE of universities declined from 0.83 to 0.78. Research-intensive universities were more efficient than professional-oriented universities. These results can help key decision-makers such as the Commission on Higher Education and universities management in identifying possibilities for improving institutional performance by identifying their strengths and weaknesses and benchmarking with their peers.