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.
Egypt started strongly, dominating the early possession from the moment Benin lost the ball from a sloppy kick-off.
El Mohamady was the surprise scorer after eight minutes, taking the ball deep on the right-hand side and whipping in a cross from more than 30 yards out.
The ball appeared to catch the breeze and instead of curling towards the waiting strikers it looped over the head of goalkeeper Yoann Djidonou, who must take plenty of blame as he failed to react.
Hossam Ghaly gave the ball away cheaply four minutes later and, with Essam El Hadari well off his line, gave Pascal Angan the chance to chip for goal.
Angan's shot had the height but with El Hadari scrambling back he was relieved to see the ball bounce wide.
After 23 minutes the lead was doubled.
Hassan produced a fine initial cross and while Djidonou did well to parry Ahmed Raouf's header, Moteab was able to slide the ball over the line from an acute angle despite a desperate attempt from the goalkeeper to claw it out.
Raouf squandered a glorious chance to head home a third before the half-hour mark, but chances for Razak Omotoyossi and Djiman Koukou brought Benin back into the game before the interval.
Moteab had a fine chance to double his own tally 10 minutes after the restart but Djidonou rushed him for time and was able to smother his shot.
Egypt received a warning shot 20 minutes from time when Rabou Hosni allowed Omotoyossi to fire at goal from six yards, but his shot was off target.
Mouftaou Adou missed an even better chance moments later when he diverted a skidding ball just wide.
At the other end substitute Mohamed Zidan was just denied after a jinking run and shot, while Moteab again missed from a fine position and Djidonou denied Rabou Hosni from a late free-kick.