The first leg will be contested on May 19, in Morocco, before the return match in Egypt a week later.
Mahmoud Kabraba’s first-leg strike was the difference between the two North African sides, with ESS unable to find the goal they needed in front of their own fans in Sousse on Sunday to take the tie to extra time.
The 0-0 draw in Tunisia was enough for the White Knights to progress to the final.
In the earlier semi-final, Berkane launched an emphatic comeback to oust another Tunisian side, CS Sfaxien, to progress.
The Sfax-based giants led 2-0 from the first leg, played at the Stade Taieb Mhiri on April 28, but Berkane responded strongly in front of their own fans at the Stade Municipal on Sunday.
Togo frontman Kodjo Fo-Doh Laba halved the deficit from the penalty spot after eight minutes, before Omar Nemssaoui levelled the contest nine minutes later.
Just after the half-hour mark, Burkina Faso defender Issoufou Dayo netted Berkane’s third to give them the advantage, dealing a killer blow from which the visitors never recovered.
Berkane, who were only promoted to the Moroccan top flight in 2012, have never won the Moroccan title, and were not expected to advance this far in the continent’s secondary club competition.