Cape Verde were awarded a 3-0 win from game played on March 24, giving them an outside chance of overhauling Tunisia at the top of African Group B, FIFA said.
FIFA also awarded Cape Verde a 3-0 win from the return, played last month, after Real Mallorca's Nsue took part in that game as well when ineligible. Cape Verde had won that game 2-1.
The decision meant that Cape Verde, previously eliminated, moved within two points of Group B leaders Tunisia who they visit on September 6 in the final group match for both teams.
Equatorial Guinea were also fined a total of 30,000 Swiss francs (£20,886).
A total of seven African World Cup qualifying matches have ended in 3-0 forfeit wins because of teams fielding ineligible players. Ethiopia, Gabon, Burkina Faso, Togo and Sudan are the teams who have previously been penalised.
FIFA did not state in what way Nsue, who was born in Spain and has played for Spain in age-restricted competitions, was ineligible.
Equatorial Guinea routinely field a mix of Spanish-based players, who qualify through their parents, and naturalised players from Brazil, Liberia, Cameroon and Cape Verde.
There has been controversy over whether the naturalised players have lived in the country for five years as required by FIFA rules.
FIFA said the decision concerning the March 24 game was originally taken by its disciplinary committee on May 7, when the result was not made public. FIFA only confirmed the decision after it was upheld following an appeal by Equatorial Guinea.