Dieumerci Mbokani scored a 10th-minute penalty and Ben Malango put the result beyond doubt in the 75th minute.
Benin, who were dreaming of reaching the third and final playoff round for the first time in their history, suffered a bitter exit after leading Group J for most of the group stage phase.
However, Hector Cuper's men, who struggled in the earlier stages of the group stage with draws against Tanzania and Benin in addition to a surprise defeat by Madagascar, made a stunning comeback and proved their strength when it mattered the most to claim top spot with 11 points, one ahead of Benin.
In the same group, Tanzania held Madagascar to a 1-1 away draw as the two teams finished third and fourth with eight and four points respectively.
Cuper, who led Egypt to the 2018 World Cup for the first time in almost three decades, will hope to repeat the feat with the Leopards when they play in the final two-legged playoff in March.
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