El Shennawy, a veteran keeper for Ahly, sustained the injury in the dying minutes of Egypt's 2-2 draw with Cape Verde on Monday.
Scans revealed the extent of the injury, confirming that El Shennawy would be unable to participate in the rest of the tournament.
The EFA issued another statement later saying that the 35-year old keeper will travel to Germany on Tuesday for further scans and treatment.
This comes as another blow for Egypt's coach, Rui Vitoria, who is already missing the services of captain and star winger Mohamed Salah due to a hamstring injury sustained in a match against Ghana last week.
Despite these setbacks, Egypt secured their place in the AFCON's round of 16, finishing as runners-up in Group B after the draw with Cape Verde.
In the upcoming round of 16 match, Egypt will face the runners-up of Group F, which includes teams such as Morocco, DR Congo, Tanzania, and Zambia
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