Mohamed Salah went down holding his leg as the Group J match drew to a close in Cairo, resumed after receiving treatment, and was almost immediately withdrawn.
Speaking after the match, Egypt assistant coach Hany Ramzy told BeIN Sports: “The initial diagnosis, according to the team doctor, is a strong muscle strain. It is not a tear, I think it is not serious.”
After scoring 44 goals in all competitions during his first season at Anfield, the striker has netted only three this term, with just one since August.
Mohamed Salah netted twice and missed two penalties when record seven-time African champions Egypt hammered Niger 6-0 last month in another qualifier.
With eSwatini (formerly Swaziland) ranked even lower than Niger, there were expectations that Mohamed Salah could get back on the goal trail at the Al Salam Stadium in the Egyptian capital.