Semi-finalists Ahli, who had gone through last week upon beating Heartland 2-1 in Cairo, rested a number of key figures and fielded fringe players instead.
The likes of Mohamed Talaat, Ayman Ashraf, Shehab Ahmed and Mohamed Shokri represented the Red Devils but were not up to scratch.
Ahmed Adel, Ahli's deputy goalie, also stood between the sticks throughout the 90 minutes and was out of form.
Conversely, Ismaili played all their available regular players and took the match quite seriously, despite the fact that they had waved goodbye to the Champions League earlier.
Abdallah Al-Shahat put the hosts ahead only after five minutes but Mohamed Barakat brought the score level in the 35th minute.
Seconds later, Ismaili regained their slender lead when Ahmed Ali got his name on the score sheet for the first time in quite a while.
Moatasem Salem ensured the coastal side's lead 20 minutes from time before Ali completed a brace four minutes later.
Talaat pulled one back for the visitors three minutes from time.
Elsewhere, Group B leaders JS Kabylie played out a 1-1 draw with Heartland in another unimportant match.
Ahli are to face Esperance while Kabylie are to take on TP Mazembe in the Champions League semi finals.
Early Opener
In Ismailia, Ahli controlled the match for few minutes after the kickoff and could have stunned the home side with an early opener.
Barakat went one-on-one with keeper Mohamed Sobhi after latching onto a Shehab through, his poor finish was no threat though.
But in spite of Ahli's promising start, it was Al-Shahat who broke the deadlock early when his well-placed effort went past Adel and into the net.
Ismaili soon became superior in terms of ball possession as the game's tempo slowed down.
Godwin also tried his luck in the 17th minute but didn't hit the target.
Ahli's summer arrival Geddo, one of the Cairo side's few regulars in the match, was replaced with Shokri after sustaining an injury on 29 minutes.
Barakat hit a sensational equalizer on the rebound from inside the area when he unleashed a fierce drive that hit the roof of the net.
But shortly afterwards, Ali connected with an Ahmed Sedik low cross to once again fire the Dervishes ahead.
Goal Deficit
Ahli revitalized for a while after the break but failed to overturn their goal deficit and conceded more goals.
Talaat, who had been quite impressive against Heartland last week, failed to convert a one-on-one chance, thanks to a brave Sobhi obstruction.
Three minutes from the hour mark, Sobhi rose to prominence again by parrying an Ayman Ashraf long-range shot.
Inexperienced defender Ashraf wasted another clear-cut chance from inside the area soon afterwards.
Ali could have added to Ismaili lead minutes past the hour mark when he capitalized on a defensive lapse from Sherif Abdul Fadil, but his close-range shot was blocked by Adel.
Salem headed Ismaili's third 20 minutes from time when he took advantage of Ahli's sloppy marking to comfortably head home a corner kick.
Ismaili took a stranglehold on the match midway through the second period, which paved the way for Ali to score his second goal with a point-blank volley.
But Talaat reduced the arrears for Ahli following a goalmouth scramble.
The match's goals