Goals from Henry Onyekuru and substitute, Moses Simon, determined Rosy Melanie's equaliser after Odion Ighalo opened the scoring spot to be only a consolation.
In what was a forgettable game, the Eagles secured top spot in their group with their fourth win of the qualifying campaign.
Odion Ighalo converted a penalty 35 minutes after Wilfred Ndidi was fouled in the box.
But the lead would last for just six minutes. Rowdy Melanie shot into an empty net after Francis Uzoho had fumbled a cross inside his area. The Nigerian shot stopper came out to claim a harmlesss cross but ended up pushing it into the part of the Seychelles player who made no mistake.
Nigeria restored their lead five minutes after the start of the second half when Henry Onyekuru, who was making his full debut, headed home from a Jamilu Collins assist.
The in form Everton man, who is on loan at Turkish side, Galatasary, was netting for the second time in eight appearances for the national team.
Nigeria passed the ball around for long periods of the game as they failed to penetrate the Seychelles defence but the Eagles will eventually get their assurance goal in the dying moments of the game through substitute, Moses Simon.
The Levente striker, who missed out on last year's World Cup due to an injury, scored with a brilliant effort minutes after replacing Odion Ighalo.
Although it was an inconsequential game, many expected the Eagles to use the game as another preparatory match for the Nations Cup which comes up in June but it was a largely disappointing show by the three-time African champions.
Gernot Rohr's men next host against Egypt in an international friendly at the terrible pitch of the Stephen Keshi stadium, in Asaba.