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.
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.

There was a complete reshuffle in central defence as Kenneth Omeruo paired Friday substitute Semi Ajayi. Also in were Frank Onyeka, Moses Simon, and Terem Moffi.
Super Eagles took the kick-off and immediately went in search of an early goal.
Two corner kicks followed a long throw-in.
The pressure led to stand-in captain Kenneth Omeruo forcing Guinea Bissau goalkeeper Jonas Mendes into a scrambling save.
But it was the home team that fashioned the first clear-cut scoring chance in the sixth minute when Frank Onyeka lost the ball but Alfa Semedo ballooned the opportunity over.
Moffi had a shot blocked for a corner in the seventh minute and in the 21st minute, after getting free of his marker in the box made a horrible connection with an attempted cross.
Osayi-Samuel, who continued at right back, powered into the Guinea Bissau box in the 30th minute and Fali Cande brought him down. Moroccan referee Samir Guezzaz immediately pointed to the spot. Simon took the responsibility and sent Mendes the wrong way to give Nigeria the lead.
The home side fashioned a scoring in the 42nd minute after Zaidu Sanusi went AWOL from his defensive position but they blew the chance as Francis Uzoho remained untested throughout the first half.
The second half was more of the same. Osimhen almost doubled Nigeria’s advantage in the 58th minute but his effort came off the post. Peseiro sent on Joe Aribo for Moffi on the hour to shore up the midfield and leave Osimhen as the lone striker.
Uzoho nearly engineered an equaliser for Guinea Bissau when he was caught dawdling on the ball. From the resultant throw, Dalcio almost found the net but the Eagles scrambled a clearance. Again in the 66th minute, Sanusi conceded space and allowed a player to get past him but Simon came to the rescue and conceded a corner.
Aribo’s goal-bound shot was expertly parried over in the 70th minute as the Eagles laboured for a second insurance goal.
Four minutes were added on but the Eagles held on to go back to the top of Group A with nine points. Their next match is away to Sierra Leone in June.