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.
The Squirrels carved out the Eagles with a number of chances in the first half; the cross bar coming to the rescue on one occasion.
The MFM combination of Sikiru Olatunbosun and Odey began to cause the home team trouble as Olatunbosun came close to giving Nigeria the lead in the 65th minute.
The Eagles struggled on a very bad pitch but continued to press the hosts as MFM FC striker Stephen Odey came in for Thomas Zenke and Alhassan Ibrahim replaced Rabiu Ali before the hour mark in a tactical substitution.
Captain/goalkeeper Ikechukwu Ezenwa pulled a good save for Nigeria before the Squirrels were awarded a penalty in the 88th minute.
And they duly took it with Mama Seibou converting from the spot to secure a crucial win.
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The home-based Eagles will entertain Benin Republic in the return leg in a week time in Kano.
The 2018 African Nations Championship (CHAN) will hold between January 11 to February 2 in Kenya.