The Nigerians fell behind after 20 minutes through a glancing header inside the six-yard box, which goalkeeper Emmanuel Daniel helped into his net.
The hosts scored again six minutes later through another header inside the box off a free kick from the left.
Coach John Obuh made three changes in the 37th minute, replacing Azubuike Okechukwu, Abubakar Aliyu and Nzube Anaezemba with Ovboka Agboyi, Chidi Osuchukwu and Moses Orkuma.
These changes galvanised the Flying Eagles and just before the start of the second half, Alhaji Gero came on for Bright Osagie and Umar Aminu replaced Oluwaseun Taro.
Gero sparked the Junior Eagles strike force. His header after 46 minutes went wide and five minutes later, his shot at goal missed target as the Flying Eagles took full charge of proceedings.
The African champions continued to dictate the pace with Uche Agbo failing to make hay when clear on goal after 65 minutes, before Gero created yet another opening only for his chip to go wide.
On 70 minutes, Metz midfielder Saliu Sodiq replaced Agbo.