Mostafa Mohamed struck five minutes from time to give the hosts a 3-1 lead on aggregate. The 22-year-old Egyptian added his second of the night soon after to wrap up the 4-1 aggregate win and pave the way for the first Champions League final between clubs from the same country.
Raja, beaten 1-0 in the first leg on 18 October, drew level on aggregate just after half-time through Ben Malango's deflected shot.
Ferjani Sassi made it one apiece on the hour mark before Mohamed's brace launched the party.
Al Ahly, who advanced to the final following victories in both legs against Wydad, are seeking a record-extending ninth crown, while Zamalek will vye for a sixth title.
The single-match final will be played on 27 November at the Borg el Arab Stadium in Alexandria.
