Fernando Varela was selected for duty in his country's fixture with Tunisia on September 7 - despite being handed a four-match ban back in March.
Cape Verde initially recorded a 2-0 victory and thought they had secured a place in the third round of qualifiers after topping Group B.
However, Fifa has now reversed the result and awarded Tunisia a 3-0 win upon discovering Varela's inclusion, meaning the Tunisians will progress to the final preliminary stage after officially winning their group.
