In the first leg of their African Nations Championship qualifier, home-based Super Eagles fell 1-0 to the Squirrels of Benin at the Stade de L'Amitie in Cotonou on Sunday.
As the Nigeria team settled into the game, they did try to hurt their host but it was fruitless as the first half ended in a barren draw.
Nigeria seized the initiative in the second half but they also failed to bury the chances they created.
As the Eagles continued to see more of the ball, Ibrahim Alhassan, in the 75th minute, waltzed his way into the box but tripped at the crucial moment.
The only goal of the game came via a penalty in the 90th minute.
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Both teams face off in the return leg in Kano on Saturday, with the overall winners qualifying for the finals taking place 11 January - 2 February 2018 in Kenya.
Captain/goalkeeper Ikechukwu Ezenwa pulled a good save for Nigeria before the Squirrels were awarded a penalty in the 88th minute.
The victor between Nigeria and Benin Republic will qualify automatically for the 2018 CHAN in Kenya.
It will be the 5th edition of the African Nations Championship, a biennial football tournament organised by the African Football Confederation (CAF) and exclusively featuring players from the respective national leagues.