Ibrahim Sangare and Sebastien Haller came closest for Cote d'Ivoire, who finished the game without midfielder, Franck Kessie, who was forced off with a back injury.
In the second half, Egypt needed their goalkeeper El Shenawy to keep them in the game.
The Al Ahli veteran made some key saves, notable amongst them was late save with his left foot to deny second substitute, Wilfred Zaha, before he was forced off with a suspected thigh injury.
In extra time, both sides had chances to net the winner but were guilty of profligacy as the game remained goalless, with a penalty shootout to decide the winner.
In the shootout, Eric Bailly, who had an excellent game, went from hero to villain as he became the only one to miss as substitute goalkeeper Mohamed Abou Gabal saved his effort before Mo Salah netted the decisive winner for Egypt.
Here are the full player ratings for the penultimate round of 16 clash.
Ivory Coast: Sangare 6; Aurier 5.5, Bailly 7, Deli 7, Konan 6; I. Sangare 6.5, Seri 5.5, Kessie N/A, Gradel 5, Haller 6, Pepe, 6.5
Subs: Die 5, Zaha 5, Boga N/A, Cornet N/A
Egypt: El Shenawy 7; El Soleyna 7, Fotouh 6, Marmoush 6, Hegazy 7; Abdelmonem 5, Kamal 5, Fathi 5, Salah 6, Elneny 5, Muhammed 5.
Subs: Trezeguet 4, Sayed N/A, Abougabal N/A, Sherif N/A