The Super Eagles won at the Stade Linite thanks to goals from Ahmed Musa, Chidozie Awaziem and Odion Ighalo in the Group E match.
This was the first-ever meeting between the Pirates and the Super Eagles. Their return game in Nigeria is set for the weekend of March 22-24.
Exciting Bordeaux winger Samuel Kalu who was handed his debut was menacing for the Eagles. He showed great pace to burst into space in the box, but his pull-back from the left by-line was put behind for a corner kick in the 13th minute.
The Super Eagles went a goal up through a brilliant strike from Ahmed Musa. His long-range, left-footed volley hit the underside of the bar and went in via goalkeeper Dave Mussard.
Former AFCON champions Nigeria were two goals up courtesy of Porto defender Chidozie Awaziem. The youngster struck from a rebound after Kelechi Iheanacho hit the woodwork from a free kick.
Nigeria were 2-0 up at the break and completely in control. The hosts offered little threat in attack.
In the 48th minute, Seychelles had a good attacking opportunity from a free kick on their right flank, but it ended with Bertrand Esther heading well off target.
The Eagles were awarded a penalty kick in the 55th minute. Musa struck on goal from a tight angle, but Mussard saved well with his legs. The advancing Kalu was fouled by Collins Esther in the box.
Changchun Yatai striker Odion Jude Ighalo dispatched the kick with ease two minutes later.
Perry Monnaie should have pulled one back for the Pirates when he beat goalkeeper Francis Uzoho to the ball but he couldn’t apply the finishing touch.
At the end of proceedings, Nigeria won 3-0. This is Nigeria’s first three points in Group E and bring them level on the log with South Africa and Libya (who are drawing 0-0 in Durban as at the time of filing this report).
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