Keet, who missed the first leg as Itumeleng Khune returned to captain the side, is suffering from a stomach bug, Matlaba is nursing a concussion, while Ngcongca has a calf injury.
Bafana drew 2-2 with the Indomitable Lions in Limbe on Saturday. Matlaba and Ngcongca both started but the latter was forced off midway through the encounter, with Rivaldo Coetzee taking his place at Stade de Limbe.
Shakes Mashaba's men are desperate for a victory tomorrow as they have two points from three games - five points less than the Group M leaders. Mauritania has six points and Gambia one point.
The match will kick off at 19h00 at Moses Mabhida Stadium.