With the Super Eagles already through, they needed just a win to ensure they finish top of Group E above South and Libya.
And they got wanted they wanted through goals from Odion Ighalo, Henry Onyekuru and Moses Simon.
It was Ighalo who gave the Super Eagles the lead in the first half from the penalty spot but a howler from Nigeria’s goalkeeper Francis Uzoho allowed Seychelles to level.
The Super Eagles regained the tie in the second half through a header from Onyekuru before Simon sealed the win with a late goal.
Gernot Rohr started two of Nigeria’s most inform defenders William Troost-Ekong and Kenneth Omeruo while Francis Uzoho returned between the post.
Wilfred Ndidi was also back and Oghenekaro Etebo was made to start in the game played in his home state.
Alex Iwobi got the No 10 role while Onyekuru, Ahmed Musa and Ighalo started in attack.
The Super Eagles quickly took control of the game but failed to open up the Seychelles defence. Iwobi was trying to make things happen and in the second minute, the Arsenal man played a short pass to Shehu Abdullahi on the right but the defender reacted slowly and his cross was deflected for a corner.
Seychelles played a quick one in the eighth minute and caught the Super Eagles napping but Uzoho had to stretch the fullest to get his hand on a dangerous cross into the box.
Despite dominating the game, the Super Eagles were failing to create clear-cut chances and Etebo had to fire over the bar twice, first from a freekick and then from open play.
Ndidi tried to take matters into his hands but his tame shot was easily collected by the goalkeeper after dribbling inside the Seychelles box.
It was in the 35th minute that the Super Eagles took the lead from the penalty spot. The referee adjudged that Wilfred Ndidi had been fouled in the box and Ighalo scored.
But seven minutes later Seychelles were level after a horror mistake from Uzoho who spilt a free kick into the path of Rody Melanie who poked home to make the 1-1 at halftime.
The Super Eagles started the second half on the front foot but just like the first half, they failed to get behind the Seychelles defence despite dominating possession.
It took the Super Eagles 15 minutes after the break to get back into the lead through Onyekuru who got his head to a cross from Jamilu Collins.
The game bore on later in the second half and not even the introduction of Paul Onuachu for his debut to partner Ighalo upfront could spark the Super Eagles.
It took Simon, an 87th-minute introduction to score in added minutes to seal the win for Nigeria.