The club has been placed into quarantine for a week by Moroccan health authorities and denied permission to travel to Cairo for the second leg, which had been scheduled to take place on Saturday.
Raja have been told to isolate their entire squad for a week and will only be authorised to leave Morocco after another series of tests.
"Faced with this situation, in order to protect the integrity of the competition and promote a spirit of solidarity, Caf agreed to postpone the return match to Nov. 1," a statement said.
The other semifinal between Raja's neighbours Wydad Casablanca and Al Ahly will be held as scheduled in Cairo on Friday.
The final will still be played on 6 November.