The seven-time champions succumbed to a 1-0 loss to the Tunisian giants under in a controversial Group A opener on Friday evening.
Star defender Ayman Ashraf received his marching orders before the 15th-minute mark after taking down Etoile striker Maher Hannachi just outside the area as he looked skip inside the area.
"The club has filed a complaint to CAF because of the injustice we suffered in the CAF Champions League in the last few years," read a statement on the club's website.
"Especially what happened against Etoile du Sahel in Rades, where the Botswanian referee made a number of mistakes that affected the outcome of the game."
The Red Devils are grouped alongside the Tunisians, FC Platinum of Zimbabwe and Sudanese giants Al Hilal.