The three-time African champions were the overwhelming favourites to win the game, but were completely outplayed by the debutants who put up a battling display all through.
The defeat cost the Super Eagles the top position in the group as they finished in second place with six points, one adrift the Barea.
The Super Eagles could also now set for a tough Round of 16 clash with perennial rivals, the Black Stars of Ghana if the Black Stars finish second in Group C, but Benin Republic and Guinea-Bissau are also in contention for that group’s second spot finish.
The Nigeria players were in a somber mood after the match against Madagaacar and scolded themselves for their horrible display.
They all resolved to put the defeat behind them and work hard to win subsequent games in order to win back the fans.
The West Africans won their opening two games against the Swallows of Burundi and Syli Nationale of Guinea before slumping to defeat versus Madagascar