It was Zamalek's fourth win in the Cup's 28 editions, which both teams have contested five times previously, with the Cairo side now having won the second most titles.
Youssef Mohamed 'Obama' Fayed headed in Zamalek's second minute opener, invigorating the noisy and more numerous Egyptian fans.
VAR was used to adjudicate a 47th minute foul by Zamalek's Mahmoud Attia that saw him shown yellow and Esperance's Abdelraouf Benguit levelled with a penalty.
But it was Bencharki who stole the night with a surgical shot in the 57th minute that electrified the near-capacity crowd at the Thani Bin Jassim ground in the outskirts of the Qatari capital.
Esperance substitute Mohamed Ali Ben Hamouda had an 86th minute effort disallowed because of a clear foul, all but sealing the result for Zamalek's jubilant fans.
Morocco's Bencharki drove home Zamalek's third and final goal in injury time.
Friday's fixture helped put to bed the chaotic clash that saw Esperance qualify, the AFC Champions League at which Wydad Casablanca abandoned the final in protest at the organisers' decision not to use VAR.
Play was stopped for more than an hour at last year's clash with the Moroccan side insisting they had not been told the video ref would be deployed.
The Court of Arbitration for Sport named Esperance the winners after a bruising legal battle that did nothing to enhance the image of scandal-tainted African football.
The Super Cup is an annual one-off match pitting the winner of the CAF Champions League and second-tier CAF Confederation Cup against each other. It was staged in Africa from its inception in 1993 until last year when it moved to Qatar.