The rankings of Africa’s top higher education institutions is provided by the 4 International Colleges & Universities (4icu). 4icu  is an international higher education search engine and directory reviewing accredited Universities and Colleges in the world. 4icu.org includes 11,160 Colleges and Universities, ranked by web popularity, in 200 countries. 
A quick look shows that South African universities dominate the top despite the fact that South Africa ranks very low on the quality of education in the world…
1  University of South Africa

South Africa
2  University of Cape Town
South Africa
3  Universiteit Stellenbosch
South Africa
4  University of Dar es Salaam
Tanzania
5  University of KwaZulu-Natal
South Africa
6  University of Pretoria
South Africa
7  Cairo University
Egypt
8  University of the Witwatersrand
South Africa
9  University of the Western Cape
South Africa
10  Obafemi Awolowo University
Nigeria
11  Makerere University
Uganda
12  University of Botswana
Botswana
13  Mansoura University
Egypt
14  Rhodes University
South Africa
15  Alexandria University
Egypt
16  The American University in Cairo
Egypt
17  Zagazig University
Egypt
18  University of Johannesburg
South Africa
19  Assiut University
Egypt
20  University of Nairobi
Kenya
21  UniversitĆ© Cheikh Anta Diop
Senegal
22  University of Zambia
Zambia
23  North-West University
South Africa
24  University of Lagos
Nigeria
25  Tanta University
Egypt
26  University of Ghana
Ghana
27  UniversitĆ© de Ouagadougou
Burkina Faso
28  UniversitĆ© Mohammed V – Agdal
Morocco
29  Nelson Mandela Metropolitan University
South Africa
30  Cape Peninsula University of Technology
South Africa
31  UniversitĆ© d’Antananarivo
Madagascar
32  Ain Shams University
Egypt
33  University of Ibadan
Nigeria
34  Kenyatta University
Kenya
35  University of Namibia
Namibia
36  Universiteit van die Vrystaat
South Africa
37  University of Nigeria
Nigeria
38  The German University in Cairo
Egypt
39  University of Limpopo
South Africa
40  UniversitĆ© de la Reunion
Reunion
41  University of Khartoum
Sudan
42  Benha University
Egypt
43  Universidade Eduardo Mondlane
Mozambique
44  Helwan University
Egypt
45  Ć‰cole Nationale d’Architecture
Morocco
46  University of Fort Hare
South Africa
47  UniversitĆ© Nationale du Rwanda
Rwanda
48  Al Akhawayn University
Morocco
49  UniversitĆ© Catholique de l’Afrique de l’Ouest
Benin
50  Tshwane University of Technology
South Africa
51  Jomo Kenyatta University of Agriculture and Technology
Kenya
52  Minia University
Egypt
53  Addis Ababa University
Ethiopia
54  Fayoum University
Egypt
55  Moi University
Kenya
56  University of Ilorin
Nigeria
57  October 6 University
Egypt
58  South Valley University
Egypt
59  Sokoine University of Agriculture
Tanzania
60  UniversitĆ© Mouloud Maameri de Tizi Ouzou
Algeria
61  UniversitĆ© Mohammed V – Souissi
Morocco
62  Al-Azhar University
Egypt
63  Kwame Nkrumah University of Science and Technology
Ghana
64  Misurata University
Libya
65  Minoufiya University
Egypt
66  UniversitĆ© d’Oran
Algeria
67  UniversitĆ© Hassan II Mohammedia – Casablanca
Morocco
68  Polytechnic of Namibia
Namibia
69  UniversitĆ© d’Alger
Algeria
70  University of Zimbabwe
Zimbabwe
71  University of Cape Coast
Ghana
72  The British University in Egypt
Egypt
73  UniversitĆ© de Tunis El Manar
Tunisia
74  University of Zululand
South Africa
75  University of Agriculture, Abeokuta
Nigeria
76  University of Malawi
Malawi
77  UniversitĆ© Cadi Ayyad
Morocco
78  UniversitĆ© Mentouri de Constantine
Algeria
79  Suez Canal University
Egypt
80  UniversitĆ© de YaoundĆ© I
Cameroon
81  Egerton University
Kenya
82  University of Swaziland
Swaziland
83  Kafr el-Sheikh University
Egypt
84  UniversitĆ© Ibn Tofail
Morocco
85  UniversitĆ© de la Manouba
Tunisia
86  UniversitĆ© Hassan II – Casablanca
Morocco
87  Covenant University
Nigeria
88  University of Benin
Nigeria
89  Ć‰cole Nationale SupĆ©rieure en Informatique
Algeria
90  UniversitĆ© des Sciences et de la Technologie Houari BoumediĆØne
Algeria
91  Durban University of Technology
South Africa
92  Strathmore University
Kenya
93  Ahmadu Bello University
Nigeria
94  UniversitĆ© Ibnou Zohr
Morocco
95  Universidade de Cabo Verde
Cape Verde
96  Sudan University of Science and Technology
Sudan
97  University of Mauritius
Mauritius
98  Muhimbili University of Health and Allied Sciences
Tanzania
99  Gulu University
Uganda
100  Vaal University of Technology