In other matches, Mamelodi Sundowns of South Africa and Esperance of Tunisia won in Algeria while reigning champions Wydad Casablanca of Morocco lost against Simba in Tanzania.
Fathy came off the bench in Cairo to double the lead for record 10-time African champions Ahly with a powerful close range shot on 84 minutes after being set up by South African Percy Tau.
Ahly, who eliminated three-time champions Raja at the same stage last season, went ahead in first half added time when Mohamed Abdelmonem headed powerfully past Raja goalkeeper Anas Zniti.
The clash of the African club titans was watched by a sell-out 52,000 crowd, most of which was dressed in the red of Ahly, who have reached five of the last six finals, but won only two.