First-half goals from Amadou Sagna and Ibrahima Niane powered the Young Lions of Teranga past the Flying Eagles with Aniekeme Okon’s effort standing as a mere consolation.
Sagna struck in the 36th minute of Monday's Last-16 tie to put Senegal in control and they doubled the lead as Niane tucked home Alpha Diounkou's cross.
Diounkou found space on the left-hand side of Nigeria's defence, crossed into the Flying Eagles’ area as Ikouwem Utin failed to stop the striker from slotting past Oremade Olawale.
Early in the second half, Paul Aigbogun’s boys halved the scoreline after the impressive Okon deflected Isacc Makanjuola’s free-kick past Dialy Ndiaye.
Nigeria pressed in search of a second equaliser but Yira Sor missed their best opportunity to level, hitting the ball off-target when faced with an open goal after Muhamed Tijani dropped a cross into his path.