Mali increased their chances of qualifying for the round, following Kenya and Uganda from a 1-1 draw in the previous match on Thursday.
Rwanda got into trouble in the 9th minute after defender Djamal Bizimana was sent off.
Mali scored two quick goals in the 19th and 20th minutes through Musa Djenepo and Ibrahima Kone.
The third-placed Kalifa Koulibally and Mali led the group with 13.4 points over Uganda.

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