Salah went off after being injured late in the game, leaving his side down to 10 men as they had already used their allotted three substitutes.
But by then Egypt were comfortably on their way to a 4-1 home win in their Group J encounter, which included a superb goal from Salah, scored directly from a corner just before half-time.
“Coach Javier Aguirre has decided to allow Salah to return to Liverpool to give him extra rest, as medical scans revealed that it would be difficult to get him fit for Tuesday's match," said an Egyptian Football Association statement on Saturday.
The statement did not indicate how long Salah might be out, but assistant coach Hany Ramzy said after Friday's game that the injury did not appear serious.
Egypt could ensure qualification for a record 24th Nations Cup finals appearance if they win on Tuesday in the southern African kingdom formerly known as Swaziland.
(Reporting by Mark Gleeson in Cape Town; Editing by Neville Dalton)
