Namibia scored through Elmo Kambindu in the 53rd minute with Micium Mhone grabbing the equalizer for the Flames in the 73rd minute.
In another match, Senegal claimed a 2-1 win over Zimbabwe.
Namibia now top Group B with seven points from three games, followed by Senegal with six points from three games. Mozambique are third with four points from three games with Malawi lying fourth with two points from three games.
Zimbabwe are at the bottom with two points from four games.