Nigeria has now advanced to the last 16 with a clean record having won all two matches in the group.
Chukwueze Simon flipped the opener deep inside the 18-yard-box in about three minutes of play from a Moses Simon assist.
Moses raced into the box and smashed a low shot to score his first goal in the tournament which was Nigeria’s third in the game.
The Sudanese had a sigh of relief when the referee after due consultation with VAR gave a penalty for a rough handle on Mustafa Mohammedís shirt by Ola Aina.
It was converted by Walieldin Khidir as he sent goalkeeper Maduka Okoye in the wrong direction to give his side a faint hope.
Nigeria was in full control despite the goal, perhaps that was a consolation goal with no intention to initiate a comeback.
Nigeria is now on top of Group D with six maximum points ahead of their final group match against Guinea-Bissau.