The Super Eagles have gone top of Group E, following a 3-2 win over Libya on Tuesday night in Sfax, Tunisia.
It is the second time that Gernot Rohr’s men have defeated the North Africans, following a 4-0 rout last weekend in Uyo.
Odion Ighalo and Ahmed Musa gave Nigeria a 2-0 lead, before Mohamed Zubya and Ahmed Benali equalized for the Mediterranean Knights.
Ighalo however struck again in the dying minutes, to ensure the Eagles got all three points.
Nigeria now have nine points from four fixtures, while South Africa are in second place with eight points.
Libya have four points and Seychelles are on one point.