Moroccan Bencharki completes weekend of losses for his country
On Saturday, Al Ahly triumphed 2-0 over Wydad Casablanca in the other first leg in Morocco through goals from Mohamed 'Afsha' Magdy and Ali Maaloul.
Record eight-time African champions Ahly and Zamalek host the return matches in Egypt on October 23 and 24 and an all-Egyptian final is on the cards.
Since the flagship African club competition debuted in 1964 there has never been a title decider featuring two clubs from one country.
Raja coach Jamal Sellami had to choose his matchday 18 without five candidates as three were injured and two forced to quarantine after testing positive for Covid-19.
The coronavirus pandemic meant both first legs were staged behind closed doors at the 60,000-capacity Stade Mohammed V in the Moroccan commercial capital.
The 18th-minute match-winner stemmed from a pin-point cross by Ahmed 'Zizo' Sayed that dipped behind Raja goalkeeper Anas Zniti and Bencharki scored with a powerful header.
Bencharki, 26, joined five-time African champions Zamalek last year from Saudi Arabian club Al Hilal after a loan spell with Lens in France.
Raja, whose last of three Champions League titles came in 1999, won plenty of possession and spent considerable time in the Zamalek half but rarely threatened to score before half-time.
They failed to take advantage of three free-kicks in threatening positions and a Soufiane Rahimi header that brought an acrobatic save from Mohamed Abou Gamal was going wide.
Starting at half-time, Sellami introduced four substitutes but Zamalek survived with Abou Gamal making several excellent saves.
Raja did have a genuine penalty appeal waved away by the Cameroonian referee in only their third Champions League meeting with Zamalek, who edged the 2002 final 1-0 on aggregate.
The coronavirus delayed the semi-finals from May until September, and Morocco requested a further postponement until October as they struggled to contain the pandemic.