It was Guinea who had the better of the opening exchanges and would have opened the scoring if it weren't for some fine goalkeeping from Mali stopper Soumaila Diakite.
However the Eagles opened the scoring just before the half-hour mark courtesy of Bakaye Traore.
The midfielder broke down the right-hand side before having a shot, which deflected in off Guinea defender Ibrahima Diallo.
Guinea threatened an equaliser and were particularly dangerous from set pieces. Former Hull City defender Kamil Zayatte headed over the crossbar while ex Celtic centre-half Dianbobo Balde also headed off target from a corner.
With the result, Mali go joint top of Group D along with Ghana, whom they face in their next match on Saturday.