The two goals were scored in the second half after Nigeria failed to convert a penalty in the early minutes of the first half.
Victor Osimhen, the highest goal scorer of the tournament produced the first goal with a powerful strike after a fast pass from the right wing, while Funsho Bamgboye who returned from two games suspension made it two after a poor throw by the Malian keeper.
It was the second time in the history of the FIFA U-17 World Cup that two African youth team would be meeting in the Final.
Nigeria beat Mexico 4-2 in the semi-final after defeating USA (2-0), Chile (5-1), Australia (6-0) and Brazil (3-0). Their only loss was 2-1 to Croatia.
Mali on the other hand, saw off Belgium 3-1 to reach the final after they went past Ecuador (2-1), Honduras (3-0), North Korea (3-0) and Croatia (1-0). They were earlier held to a goalless draw by Belgium.
With this victory, the Golden Eaglets have now won the competition a record five times.