The win over Congo has boosted the African Champions’ chance of qualifying for the tournament that will hold in Equatorial Guinea next year.
Nigeria is now second in Group A with seven points while South Africa still leads the group with 11 points from five games.
Two second half goals from striker Ike Uche from the penalty spot and Aaron Samuel ensured Nigeria moved to second spot in the group.
The Eagles now need a win over South Africa to seal their place amongst the 16 teams that would compete in Africa’s biggest football tournament.
It was a hard earned victory for Nigeria, with Godfery Oboabona’s jersey torn while Azubieke Egwueke had his head bandaged.
During the game, Congolese fans threw different materials into the pitch, as Nigeria raced to the two-goal lead.
The development led to a temporary suspension of the game for over six minutes.
The Congolese side had defeated the Super Eagles in the first leg of the game in Calabar. They now stand at the fourth position with seven points while Sudan is at the bottom of the table with 3 points from five games.