The Super Eagles will take on Guinea Bissau next in their final group game on Wednesday.
The Eagles went into first half break with a 2 goal lead, leaving Sudan with a huge mountain to climb.
Nigeria international Samuel Chukwueze was on target for Villarreal as the visitors thrashed Switzerland’s Young Boys 4-1 in their Champions League group stage.
The Yola-born 23-year-old striker is a product of an Abuja based football academy.
Nigeria leads Group L with 15 points with Benin Republic coming second and both qualifying for the 2021 AFCON to be hosted by Cameroon.
