Going into this match trailing 2-0 from the first leg, Simba SC reduced arrears after just 15 minutes through Zambia international Joshua Mutale, who smashed home from an acute angle after being set up by Elie Mpanzu.
Simba's efforts to successfully stage a comeback were dealt a blow when they went a man down when midfielder Yusuph Kagoma was red-carded five minutes into the second half.
The Tanzanians also saw Fadlu Davids' assistant coach Darian Wilken seeing red.
Towards the end, Simba thought they had drawn level through Steven Mukwala, but his headed goal was adjudged to have been scored from an offside position after a VAR check.
The match was killed as a contest in stoppage time when substitute Soumaila Sidibe equalised for Berkane, leaving Simba needing to score three goals without reply to be crowned champions.
It then ended 1-1 on the afternoon and 3-1 on aggregate in favour of Berkane, who now have three Confederation Cup titles.