The country appealed the ruling to remove it from the final stages of CAF qualifying for fielding an ineligible player, but the initial sanction has been upheld.
Cape Verde has lost its appeal to the Court of Arbitration for Sport against FIFA's decision to expel it from World Cup qualifying.
The Africans were kicked out of the final stages of the CAF qualifying competition for Brazil 2014 for fielding an ineligible player in the win over Tunisia in September.
They had topped Group B of African qualifying after their 2-0 win in Rades. However, FIFA found the Cape Verdean Football Association guilty of fielding Fernando Varela, despite the defender not having served a full four-match suspension for a red card.
As a result, Tunisia was awarded a 3-0 win — enough to move it on top ahead of Cape Verde and into a two-leg playoff clash with Cameroon.
Cape Verde appealed the original ruling, but its case was dismissed early in October — prompting the nation's FA to take the issue up with the CAS.
A statement from CAS read: "The Court of Arbitration for Sport (CAS) has dismissed the appeal filed by the Cape Verdean Football Federation (FCF) against the FIFA Appeal Committee (the FIFA AC) decision of 23 September 2013.
"In such decision, the FIFA AC entirely confirmed an earlier decision of the FIFA Disciplinary Committee (FIFA DC) in which the FCF was found to have fielded an ineligible player during a FIFA World Cup qualifying match against Tunisia and sanctioned with the loss of the match 3-0.
"Consequently, the results of the qualifying rounds for the FIFA World Cup 2014 remain unchanged."