Sudanese side Al Merreikh beat Ghana's Asante Kotoko 2-1 to grab second place on goal difference. Tunisian side Etoile du Sahel reached the final of the 2008 Confederation Cup after beating Algeria's JS Kabylie 2-0 last Saturday.
The win in Sousse took the home side to the top of Group B with 10 points in the last round of group matches, while JS Kabylie eventually dropped to third in the group with nine points.
Etoile were determined to seal the top place in the group and took the lead through Ammar Jmel on 11 minutes.
But the home side had to wait until injury time before Mohamed Ali Nafkha made it safe with the second goal for the Sousse side.
Etoile, who won last year's Champions League, will know their opponents for the final after the match between defending champions CS Sfaxien and Tunisian rivals Club Africain in Group A, which was to be played last night.
The two group winners go straight through to a two-leg final in November with a US$330,000 first prize on offer.