A banner displayed in the stands reportedly read: “You lack national team spirit. Mané came to play here.”
Salah did not travel to Juba for the Group B encounter after the Egyptian Football Association confirmed that he would be rested because of concerns over the artificial playing surface at Juba National Stadium.
Egypt coach Hossam Hassan subsequently said the decision had been agreed with Salah before the team's opening qualifier against Angola, with the player's safety given as the priority.
Hassan also dismissed speculation that Salah’s absence was linked to tensions following his substitution during Egypt’s goalless draw with Angola.
“We decided to rest Salah because of the artificial pitch,” Hassan said, adding that the former Liverpool and Egypt star remains an important member of his plans.
Some South Sudan supporters nevertheless expressed their disappointment at not seeing the Egyptian captain in Juba, using the presence of Senegal forward Sadio Mané in previous matches as a comparison.
The incident added an extra talking point to the AFCON 2027 qualifier, with Egypt facing South Sudan without one of their most prominent players.