The Dervishes were below-par throughout the game but managed to snatch a hard-fought victory, to recover from their disappointing 2-1 defeat to Masri last week.
The victory put Ismaili in fourth place of the league table with 22 points, five adrift of leaders Ahli, who have a game in hand. Mahalla lie seventh on 17 points.
Mohamed Ateya stunned the home crowd on the quarter-hour mark with a brilliant strike.
The striker collected a long ball on the edge of the area, flicked it while turning and sent a curling right-footed shot into the far corner of the net.
Iraqi striker Mostafa Karim notched his seventh goal in the league campaign to level the score in the 29th minute.
He capitalized on a sloppy defending to drill in a low cross from the right.
Ismaili mounted pressure on the visitors but rarely created clear-cut chances.
Winger Ahmed Samir Farag went close seven minutes after the interval but his fierce shot cannoned off the crossbar.
Fadl finally scored the precious winner two minutes from time when he connected with Hosni Abd-Rabou's cross at the near post to head home.