Musa opened scoring in the 15th minute with a cracking volley from outside the 18
Meanwhile Debutant Samuel Kalu was a handful for the Pirates with his trickery and pace although his end product was at times lacking a little
The Eagles were 2-0 up just before halftime when Chidozie Awaziem fired in a rebound after Leicester City forward Kelechi Iheanacho hit the post with a shot from free kick
China based Odion Ighalo ended an goal drought when he stepped up to take and convert a penalty in the 55th minute after Samuel Kalu was fouled in the box
Seychelles went close to reducing the tally late on in the game as Perry Monnaie beat goalkeeper Francis Uzoho to the ball, only to send it wide off the target.
Semi Ajayi and Henry Onyekuru both came on as late subs as the Super Eagles ended the game victorius.
Seychelles XI: Dave Mussard, Jones Joubert, Bertrand Esther, Benoit Marie, Jude Nancy, Warren Mellie, Carl, Colin Esther, Darren Pamod, Nelson Laurence, Perry Monnaie
Subs: Jerome Dingwall, Elijah Tamboo, Gervais Waye-Hive, Kiren Sinon, Colyn Francourt, Juninho Mathiot, Colin Bibi
Nigeria XI: Francis Uzoho, Kenneth Omeruo, Leon Balogun, Chidozie Awaziem, Brian Idowu, Ogenyi Onazi, Wilfred Ndidi, Kelechi Iheanacho, Ahmed Musa, Samuel Kalu, Odion Ighalo
Subs: Ikechukwu Ezenwa, John Ogu, Oghenekaro Etebo, Simeon Nwankwo, Semi Ajayi, Joel Obi, Henry Onyekuru.