The performance of a university depends on departmental activities in a network framework. The university is efficient only if these departments are efficient in their operations. The connection between departments is fundamentally complicated and should be scrutinised to offer more suitable ways for more enhancement. However, to our knowledge, no single study exists which assesses the performance of South African universities in a network structure accounting for the effects of exogenous factors on the overall and structural efficiencies. Our study employed the network-based DEA method to examine the performance of South African higher education institutions in a network structure of teaching and research for the period 2009/10-2016/17. The findings reveal that the efficiency of teaching activities is 0.942, while the efficiency of research operations is 0.782. The network-based performance of South African universities is 0.844, strongly associated with research efficiency. The findings also reveal that the percentages of staff with PhD and Master's degrees and professional staff, student fees, personnel grant, and government funding influence the efficiency of research activities. A definite need for government organisations and other higher education-related stakeholders should incorporate these findings to strategies for National Development Plan 2030 targets.