The Islanders have been disqualified from the final preliminary stage after they included a suspended player in Sunday's victory over Tunisia
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.
The draw for the third round of qualifiers is scheduled to take place on Monday, September 16 and will be played over two-legged ties to determine who secures a ticket to Brazil next summer.