Adamu Alhassan scored the only goal of the encounter.
The Flying Eagles missed an opportunity to score an early goal when Nafizi Yahaya missed their only clear-cut chance of the first half in the fourth minute.
In the second half, the seven-time winners of the competition continued their unimpressive display until the 51st minute when Mohammed Jamil’s header forced a brilliant save from the Nigerien goalkeeper.
The Flying Eagles, however, broke the deadlock in the 73rd minute through Alhassan’s free-kick which beat the Niger goalkeeper to hand Aigbogun’s side their second win in the competition.
Nigeria finished top of Group A with seven points, while South Africa who beat Burundi 1-0 in the other matchday three encounter are second with five points.
They also advanced to the semi-finals and booked a spot at the 2019 FIFA Under 20 World Cup.
Niger Republic and Burundi both crashed out of the competition after the hosts finished third with two points, while Burundi finished at the bottom of log with one point.
The Flying Eagles will now face the runners up in Group B in the semifinals on Feb. 13, while the Amajitas of South Africa clash with Group B winners Senegal.
Ghana and Mali occupy second and third spots in Group B and are both in contention for a second place finish having been tied on the same points.
The 2019 Africa Under-20 Cup of Nations which is in its 15th edition kicked off on Feb. 2 and is expected to end on Feb.17.