The final ended 2-2 on aggregate following the return in Cairo with the Egyptian giants taking the trophy after scoring an away goal in last Sunday's 2-1 first leg defeat in Morocco.
Hamdy swept the ball home after 23 minutes when Berkane failed to clear a corner but there were chances for both clubs to add more goals.
The Moroccan side finished down to 10 men when defender Hamza El Moussaoui was sent off in added time.
Sunday’s victory ensured Zamalek’s second success in the Confederation Cup. They beat Berkane on penalties after drawing the 2019 final 1-1 on aggregate.
Egypt can complete a double in the African club competitions on Saturday when Zamalek's arch domestic rivals Al Ahly host Esperance of Tunisia in the Champions League final second leg. The first leg in Tunis on Saturday ended goalless.
