Zamalek secured a 5-1 aggregate triumph and will meet arch-rivals Al Ahly in the final in Alexandria on Nov. 27, a clash between the two most successful sides in African club competition.
The second leg, originally scheduled to be played in October, had been twice delayed when up to 16 Raja players tested positive for COVID-19.
Zamalek led 1-0 from the first leg in Morocco but Raja, last in the final of the continent's top club competition 18 years ago, levelled on aggregate when Congolese striker Ben Malongo had a shot deflected into the back of the home side's net.
Zamalek, who started in an ultra-defensive formation to preserve their first-leg lead, then came out to play and equalised through Ferjani Sassi just after the hour mark.
Mohamed powered home a header to extend the lead in the 85th minute and added another four minutes later.
Bencharki completed the late rout in stoppage-time as Raja's defence crumbled.
Zamalek have won five Champions League titles compared with the record eight for their Cairo rivals Al Ahly.