Patson Daka rammed home with just six minutes inside this tense and hotly contested clash before Wayne Museba headed Musonda Siame's corner in the 17th minute.
Zambia, who lost their opener 0-1 to Guinea were full of drive and fought bravely in the second half to hold off a young Menas charge. But a 65th minute volley by Malick Saidou Gonda gave Niger a huge lifeline and they poured forward in search of second. Zambia held firm and in the closing stages Patson Daka and Enock Mwepu could have added a third but their efforts went wide off the goal.
With the second straight loss, Niger can longer qualify to the semi-finals at the end of their final group A clash against Guinea who have four points. Nigeria, also on four points, play Zambia at the Stade Municipal with the winner of the clash guaranteed a place in the last four and a place at the FIFA Under-17 World Cup Chile in October.