They will contest their first continental cup final next month against Morocco's Royal Armed Forces who secured first place in Group A last month.
Ismaili had to win to have any chance of finishing top but spent most of the time defending as goalkeeper Mohamed Sabri made a string of saves to deny Dolphin's strikers including stopping a Kennedy Chinwo penalty three minutes from time.
Dolphin FC who finished three points ahead of their Egyptian rivals host the first leg of the final on the weekend of November 4-6 with the return in Rabat on November 18-20.
Royal Armed Forces confirmed their dominance in Group A with a 1-0 win at Guinea's Fello Star Labe in Conakry on Saturday.
The military side Morocco's league champions finished four points clear of King Faisal Babes of Ghana in their group.