Wolves forward Bakary Sako gave Mali the lead in the 52nd minute, producing a fine first touch to create space for himself in the area before hammering home.
The hosts' bid for three points could have been derailed when Samassa was given his marching orders in the 63rd minute, the goalkeeper handling the ball outside his area to earn a straight red card.
Mali, winners of the tournament in 2002, eventually made sure of the win in second-half stoppage time as Bordeaux man Cheick Tidiane Diabate beat the Malawian goalkeeper in the air and nodded into the empty goal.
Sunday's match in Bamako had been scheduled for Saturday but was moved back following torrential rain.
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