The pair will not travel with the rest of the team to Cameroon on Saturday.
EFA announced on Friday that Wael Gomaa, three-time Africa Cup of Nations champion, will be the new national team director.
Salah was so close to winning the 2017 Africa Cup of Nations title in Gabon but Egypt lost the final to Cameroon 2_1 after they were leading the game 1_0.
Uganda plays in Group A alongside Egypt, Democratic Republic of Congo and Zimbabwe.
Ismaily's poor results at the league werethe main reason behind his decision to leave the club.
The goalkeeper turned 45 in January and he will be the oldest player ever to participate in the tournament if he plays in the World Cup.
Shikabala continued his amazing run with his team, scoring his sixth goal in the league this season.
Salah scored two goals in a 2-1 victory over Congo on Sunday, October 8, to secure Egypt’s qualification to the World Cup.