Samuel Chukwueze gave Nigeria the lead after just three minutes, and Tayo Onyi added the second goal at the end of the first half.
Moses Simon made the score 3-0 after 36 seconds of the break, while Wali El Din Khader scored Sudan’s goal from a penalty kick in the 70th minute.
Nigeria leads the group with six points, having previously won 1-0 against Egypt in its first match.
Sudan’s balance stopped at one point in two matches, after a goalless draw with Guinea-Bissau, and it needed to beat Egypt in the last match to maintain its hopes of qualifying.
Later in the day, Egypt will play Guinea-Bissau for the same group (fourth).
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