Berkane, who are based in the citrus-producing northeast of the kingdom, also reached the final last year before losing on penalties to Zamalek of Egypt.
Midfielder Aziz put the 'Orange Boys' ahead on 20 minutes and defender Imad Kimaoui levelled for the 'Gazelles' 10 minutes later.
The match-winning goal came on 61 minutes as Aziz once again beat goalkeeper Abderrahmane el Houassli from the penalty spot.
Berkane will play Pyramids of Egypt or Horoya of Guinea, who meet Tuesday in Casablanca, in the final this Sunday.
Pyramids have been playing an average of two matches a week since August when the Egyptian Premier League resumed after a lengthy coronavirus-induced shutdown.
Horoya have been far less fortunate, relying on individual and group training since mid March when football was suspended in Guinea.
Covid-19 has severely disrupted the Confederation Cup, the African equivalent of the UEFA Europa League.
The two-leg semi-finals and single-match final were scheduled for May, then the format was changed to singles matches in Morocco and pushed back to September because of the pandemic.
A Covid-19 spike in the kingdom necessitated a further delay to this week in a competition that has been dominated by north African sides.
Clubs from Tunisia (five titles), Morocco (four) and Egypt (two) have won 11 of the 16 editions since the competition kicked off in 2004.