The Pharaohs had already qualified for the last 16, but the Liverpool forward broke the deadlock in Cairo with a perfectly-executed set-piece in the 36th minute.
It was Salah's second goal of the tournament as Ahmed Elmohamady then doubled the hosts' advantage shortly before half-time to ensure a first-place finish in Group A.
Meanwhile, Naby Keita was unused substitute in Guinea's 2-0 victory against Burundi earlier on Sunday that keeps alive their hopes of reaching the knockout rounds as one of the best third-place teams.