Ellis was in Rabat to collect the prestigous prize at the CAF awards ceremony on Thursday evening.
The South African tactician has already guided Banyana to a spot in Women's Africa Cup of Nations final on Sunday, while they have also qualified for their second FIFA Women's Women World.
Ellis was not the only representative from South Africa to collect an award after Mamelodi Sundowns Ladies were named Women's Club of the Year.
Sundowns were the inaugural winners of the Women's CAF Champions League last year after defeating Ghana's Hasaacas Ladies in the final.
28. Kaizer Chiefs (South Africa)
18. Orlando Pirates (South Africa)
10. Wydad AC (Morocco)
9. CS Sfaxien (Tunisa)
8. Al Hilal (Sudan)
7. Etoile du Sahel (Tunisia)
6. Al-Merreikh (Sudan)
4. Zamalek (Egypt)
3. TP Mazembe (DR Congo)
2. Esperance (Tunisia)
1. Al Ahly (Egypt)
5. Mamelodi Sundowns (South Africa)