Defending champions Egypt completed their Group C campaign with a third win from three as first-half goals from Ahmed El Mohamady and Emad Moteab ensured Benin's elimination from the competition.
Benin needed to win and for Nigeria to lose to stand any chance of progressing but Egypt scored through El Mohamady's (right)fortunate goal after only eight minutes to ensure that was never likely.
Moteab squeezed home a second from a tight angle but despite plenty of chances there were no further goals.
Nigeria join them in the quarter-finals after a brace from Peter Odemwingie set them on their way to a 3-0 win over Mozambique.
The Lokomotiv Moscow forward scored in the 45th and 48th minutes, before substitute Obafemi Martins sealed victory with a late strike to hand under-fire head coach Shaibu Amodu a welcome boost in fortunes.
The Super Eagles boss had been feeling the pressure since losing to Egypt in the opening game.
Benin and Mozambique end their African Cup of Nations campaigns with just a point apiece. Egypt will play the runner-up in Group D, while Nigeria face the winner.
Gabon lead Group D with four points, one ahead of Cameroon. But both third-placed Tunisia and fourth-placed Zambia can still qualify, however. Cameroon, who have also qualified for the World Cup in South Africa, need to beat Tunisia today to ensure a place in the quarter-finals.