The seven-time champions were made to work hard by the Cheetahs, who exit the tournament with heads held high after a historic campaign that included their first open-play win at AFCON and an end to a long winless run in the competition.
Egypt dominated the early exchanges and almost struck inside eight minutes when Mohamed Salah released Omar Marmoush with a superb pass from deep. Marmoush, however, was denied by the quick reactions of goalkeeper Marcel Dandjinou. Benin responded with a long-range free kick from Junior Olaitan that was comfortably handled by Mohamed El Shenawy.
Clear chances continued to fall Egypt's way. Salah was crowded out at the near post after Mohamed Hamdi's cross, while Rami Rabia later saw a close-range effort blocked on the line. Benin were dealt a blow midway through the first half when striker Aiyegun Tosin was forced off injured, and Egypt also suffered misfortune as Hamdi had to be stretchered off just before the break.
The tempo increased after halftime, with both goalkeepers called into action. El Shenawy denied substitute Jodel Dossou from close range, while Dandjinou stood firm to keep out Salah's chipped effort following a clever ball from Zizo.
The breakthrough finally arrived in the 69th minute through a moment of quality. Mohamed Hany pulled the ball back from the byline and Marwan Attia smashed a first-time strike into the top corner from the edge of the area. Benin refused to fold and found an equaliser seven minutes from time when Dossou reacted quickest after El Shenawy failed to clear Olaitan's cross.
With the match heading into extra time, Egypt regained control. In the 97th minute, Attia again played a key role, picking out Yasser Ibrahim, who looped a header over Dandjinou to restore the Pharaohs' lead. Benin pushed forward in search of another response but were unable to capitalise on late set-piece opportunities.
Salah put the result beyond doubt in the dying moments of extra time, racing clear on a counter-attack after a Benin corner and scoring from distance with Dandjinou stranded. The goal was Salah's 10th at AFCON finals, making him the third Egyptian to reach that milestone.
Egypt now turn their focus to Saturday's quarter-final at the same venue, where they will face either Ivory Coast or Burkina Faso, while Benin bow out after an admirable and memorable tournament run.
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