Egypt, who won 2-1 in their opening match in Congo last month, sit firmly on top of Group E with six points while Ghana are now at serious peril of failing to qualify with just four more games to come.
Ghana full-back Harrison Afful brought down Mahmoud Trezeguet in the box two minutes before the break and Roma forward Salah made no mistake from the resulting penalty, calmly converting into the middle of the goal.
Ghana came back strongly after half-time, with Egypt’s 43-year-old goalkeeper Essam Al Hadari forced into making key saves from Christian Atsu just after the hour mark and Emmanuel Agyemang Badu in the 79th minute.
However, Saied finished off a counter-attack with five remaining to seal victory for Egypt, who are bidding for a first World Cup spot since 1990.
Victory secures revenge for the Pharaohs, who were heavily beaten by Ghana in a qualification play-off for the 2014 World Cup.