Mohamed Salah score to secure a 1-0 home win but fans of the Pharaohs were left sitting on tenterhooks for the most part as their side played on the back-foot.
After matchday four, the 2017 Afcon finalists sit two points clear at the top of Group E ahead of games against Congo and Ghana.
“Everybody knows that I defend [coach Hector] Cuper but I’m very disappointed," former Egypt striker Ahmed Hossam 'Mido' told ONSport satellite channel.
"Egypt’s performance [has not] developed under Cuper’s leadership.
“The Egyptian Football Association must look at the situation differently.
"We have two games against Congo and Ghana to qualify for the World Cup and they should worry about the national team.
“We lack the characteristics of champions.
"Cuper must understand that our dream is to reach the World Cup, put in good performances and control the games, and this [hasn't] happened lately.
“Our performance against Uganda is alarming and I should warn the EFA."
Egypt host Congo next month before playing as guests to Ghana on the final matchday.
The Pharaohs' last visit to Ghana ended in a 6-1 annihilation in the qualifying playoff first leg for Brazil 2014.
The Pharaohs, having twice played at the World Cup, are hoping to make a return to the global showpiece for the first time since 1990.