Both teams were on level terms when a tame cross-come-shot from Hodoud's Mohamed Hamed squirmed through Al-Hadari's hands and legs on 112 minutes.
The 37-year-old shot-stopper, who will be suspended for four months starting next season for breaching his contract with Ahli in 2008, was instrumental in helping the Dervishes reach the semi finals.
In the penalty shootout against Ittihad, Al-Hadari denied a spot kick before converting Ismaili's last to give them a 5-3 quarter-final win.
In Thursday's game, Islam Al-Shater broke the deadlock one minute past the half-hour mark when he came unmarked to latch onto an Ahmed Saied 'Ouka' free kick and slot home from close range.
Ismaili's Tunisian striker Mohamed Selliti equalized a couple of minutes later with a point-blank volley, connecting with a Mohamed Hommos header.
Title holders Hodoud will take on league winners Ahli, who defeated Military Production 2-1 later in the day, in the Egyptian Cup final on Monday at Cairo Stadium.