Faced with limited resources, scientists from around the world enter into collaborations to join their resources to conduct research. Like everywhere else, international co-publishing in southern African countries is increasingly on the rise. The aim of this study was to document and analyse the level of scientific productivity, collaboration patterns, scientists' experiences and attitudes towards South-South and South-North collaboration. We performed 105 interviews with scientists based at five southern African Universities, namely; University of Malawi-Chancellor College, National University of Science and Technology, the University of Botswana, the University of Zambia, and the University of Zimbabwe. We also traced 192 scientists from the various departments at these universities that had jointly published 623 scientific papers in the field of basic sciences in the period 1995-2014 in Web of Science journals. Our results show that in the majority of the cases funding from the North contributed substantially to increased scientific productivity, and international co-authorship. The results also show that collaboration with southern scientists is equally valued as that with northern scientists, but for different reasons. We conclude that supporting international and national collaboration which includes increased scientific mobility, strong scientific groups and networks, are key factors for capacity building of research in southern African Universities.