Ange Martial Tia put the Eagles ahead after only five minutes, finishing from Lassine Sinayoko’s pass. Cape Verde levelled five minutes later when Sidny Lopes Cabral scored from a free-kick.
Dorgeles Nene restored Mali’s lead in the 39th minute, set up by Amadou Haidara, to send the hosts in 2-1 at the break.
Nene completed his brace in the 51st minute. Kamory Doumbia released him on the counter and the forward finished with his right foot. That goal settled the contest. Cape Verde created little after the interval as Mali managed the game.
The result gives coach Anthony Da Silva a winning start. Mali controlled more of the ball and produced more shots on target. Aliou Dieng was booked late on; Cape Verde’s Roberto Lopes and Kevin Pina were also cautioned.
Mali sit on three points alongside Rwanda, who beat Liberia 3-1 on the same matchday. Cape Verde and Liberia have none.
The Eagles next travel to face Liberia on Tuesday, 29 September. Cape Verde meet Rwanda the same day. The group winners and a set of runners-up will join hosts Kenya, Tanzania and Uganda at the 2027 finals.
For Mali it was a statement opening. For the Blue Sharks, a first-night defeat leaves little margin in a tight four-team section.