Nigerian came back to revenge a home defeat to Guinea-Bissau, recording a 1-0 win against same opposition on Monday.
The Djurtus shocked everyone on Friday when they recorded a 1-0 victory over the Super Eagles in Abuja.
However, a first-half penalty from Moses Simon was enough for Jose Peseiro’s men to win the reverse fixture.
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With the result, Nigeria return back to the top of Group A with nine points with two more points than second placed Guinea-Bissau.
The slim victory also ended a four-match losing streak for the Nigerians who have won the AFCON three times.
The third place is occupied by Sierra Leone with five points, while Sao Tome & Principe sit at the bottom of the group with just one point.