The study used Link Analysis to compare Kenyan and South African universities according to several Web-based indicators, some of which include the number of pages, and the number of in and out-links. The authors examined the external out-links in order to determine the institutions targeted by South African and Kenyan universities. Also investigated were the networks or links between universities. Web Impact Factors (WIFs) were calculated and reported in order to compare the universities’ web influence. Results indicate that Kenyan universities, like most African universities, have embraced the Internet and its constructs fairly recently, hence most of their websites are at initial stages of construction. Comparatively, South African universities have made remarkable progress in their web presence, which is at an advanced stage of development, equaling counterparts in more developed countries. The study recommends that regional webometric studies be conducted periodically in order to investigate and map the web-related developments of African universities. It concludes that African universities, though not comparable to counterparts in developed countries, can have their websites evaluated webometrically.