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 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 Shaibu Amodu a welcome boost.
The Super Eagles boss had been feeling the pressure since losing to Egypt in the opening game.
Benin and Mozambique end their African Nations Cup campaigns with just a point apiece.
Source: PA
