Sudanese striker Mohammed gave the Falcons the lead in the 31st minute of the game to peg the Flying Eagles back.
The first half ended with the Sudanese in front but Nigeria was a totally different proposition in the second half.
Victor Osimhen was proving to be a handful for the Sudanese defenders who struggled to cope with his pace. Samuel Chukwueze eventually pulled Nigeria level, scoring the leveller in the 67th minute.
The winger nearly made it a brace eight minutes later but he failed to hit target as Nigeria began to assert themselves.
The turnaround was complete when Osimhen got rewarded for his brilliant performance with a well-taken goal with four minutes left in regulation time to give Nigeria a cushion heading into the second leg.