Togolese Laba, the leading goalscorer in the African second-tier club competition with eight, was the architect and executioner as the hosts made a stoppage-time breakthrough.
The tall striker, who had been generally well policed by the Zamalek defence, ran on to a long pass out of defence and darted toward the goalmouth.
With two defenders in hot pursuit, Laba passed to Hamdi Laachir, who pushed the ball back into the path of the west African and he hammered the ball into the roof of the net.
The goal was a massive relief for the dominant home side, who were foiled twice by the woodwork in the first half before a near-capacity crowd in the 15,000-seat Stade Municipal.
Zamalek were frequently guilty of time wasting and seemed more intent on not losing than winning as they seek a first African trophy since 2003.
The Egyptians were forced to start with third-choice goalkeeper Omar Salah because regular Mahmoud 'Gennesh' Abdel Rahim was suspended and reserve Emad el Sayed injured.
Zamalek registered three goalkeepers for the African equivalent of the UEFA Europa League with Omar el Said, who started as the lone striker, the emergency back-up shot-stopper.
Abdel Rahim will be available for the return match in Egypt next Sunday when the destiny of the $1.25 million (1.1 mn euro) first prize will be decided.
The first leg marked the debut of the video assistant referee (VAR) system in the Confederation Cup and the Zambian referee used it once, to dismiss a Berkane penalty claim.
Zamalek started the final as slight favourites given they have contested 12 CAF finals, winning nine, while Berkane were appearing in a final for the first time.
The Moroccans had scored 21 goals in seven home matches en route to the title decider while Zamalek kept five clean sheets in seven away outings.
Berkane were superior in the opening half and unlucky not to be ahead by half-time with headers from Laba and Samir Ouidare rebounding off the woodwork.
Zamalek temporarily shed a defensive stance to twice almost take the lead with Berkane goalkeeper Abdelali Mhamdi foiling Youssef Ibrahim, and Mahmoud Kahraba firing wide.
Berkane responded to these scares with a series of attacks and Salah saved acrobatically two minutes from time to prevent Laba breaking the deadlock.
But the Egyptian goalkeeper was powerless to stop the 27-year-old Togo international scoring the dramatic winner that leaves the all-north African final delicately balanced.