Mokoena dropped by Mosimane
The Portsmouth man, who can play in defence or midfield, has not started any of the last seven matches for the Championship club and his lack of first-team football is thought to be one of the main reasons for his axing.
Elsewhere in the 24-man list, there is a recall for Katlego Mphela - the Mamelodi Sundowns striker who was not selected for a recent friendly against Kenya after absconding from his club.
Head coach Pitso Mosimane also called up Wayne Sandilands from Sundowns as the No2 goalkeeper following a season-ending injury to Orlando Pirates' Moeneeb Josephs.
"We are playing at home and our main aim is to get three points," Mosimane said. "We should not underestimate our opponents because of the current standings in the table and the fact that their country has been unstable.
"In fact, they will be more dangerous as they believe this is the time to win and get their campaign back on track. The Egyptian team have been working hard at training. They have played six more matches than us in preparing for this clash with us, so we need to be extra careful in our approach."
Tottenham Hotspur pair Bongani Khumalo and Steven Pienaar are both named, along with Leeds United forward Davide Somma, who only recently chose to represent the country of his birth.
Bafana Bafana currently head Group G with four points from two games, three more than the Pharaohs ahead of the fixture at Ellis Park on 26 March.
South Africa squad:
Goalkeepers: Itumeleng Khune (Kaizer Chiefs), Wayne Sandilands (Mamelodi Sundowns), Darren Keet (Bidvest Wits)
Defenders: Siboniso Gaxa (Lierse SK), Morgan Gould (SuperSport United), Anele Ngcongca (Genk), Siyabonga Sangweni (Golden Arrows), Mzivukile Tom (Golden Arrows), Bongani Khumalo (Tottenham), Rueben Cloete (Orlando Pirates)
Midfielders: Siphiwe Tshabalala (Kaizer Chiefs), Reneilwe Letsholonyane (Kaizer Chiefs), Sifiso Myeni (Bidvest Wits), Thanduyise Khuboni (Golden Arrows), Steven Pienaar (Tottenham), Andile Jali (Orlando Pirates), Tlou Segolela (Orlando Pirates), Daylon Claasen (Lierse SK), Kagisho Dikgacoi (Fulham), Thulani Serero (Ajax Cape Town)
Forwards: Davide Somma (Leeds United), Bernard Parker (Panserraikos), Kermit Erasmus (SuperSport United), Katlego Mphela (Mamelodi Sundowns)