Akinkunmi Amoo shot Nigeria into the lead in the 43rd minute. Amao almost doubled Nigeria’s lead in the 48th minute but saw his effort blocked.
Olakunle Oluwasegun doubled Nigeria’s lead in the 58th minute.
Four minutes into added time, Niger Republic scored a consolation goal.
Oluwasegun was named man of the match.
The five time world champions will now face Ghana, who defeated Ivory Coast 2-1. The West African neighbours will meet in Niamey on Saturday.
The 2019 Africa U17 Cup of Nations tournament will take place in Tanzania.