The disappointing result is likely to increase pressure on Ismaili coach Emad Soliman, who was recently given a vote of confidence by the club's board.
The last season's runners up slipped to fourth place on 33 points, behind third-placed Zamalek, who defeated Petrojet 3-1 in another rescheduled match earlier in the day, on goal difference.
Ismaili are seven points behind holders and leaders Ahli, who are favorites to win a sixth consecutive league title.
ENPPI, who have won one game out of four since the appointment of Bulgarian coach Stoycho Mladenov, are ninth on 25 points.
Ismaili had to do without Egypt keeper Essam Al-Hadari, who started a strike in protest against the club's failure to fulfill their financial obligations towards him.
They managed to take the lead after seven minutes when midfielder Abdullah Shahat robbed Abdul-Aziz Tawfik on the edge of the area and drilled a low shot into the bottom corner.
ENPPI then piled on pressure and wasted several clear-cut opportunities to level the score, with Ivorian striker Zeka Goore wasting most of them.
Their best chance fell to striker Ahmed Abdul-Zaher few minutes after the restart but he blasted the ball wide with the goal at his mercy.
ENPPI's pressure paid dividends in the 63rd minute in bizarre fashion.
They were initially awarded a penalty after Ismaili defender Ibrahim Yehia clumsily felled winger Islam Awad.
Mohamed Sobhi, who deputized for Al-Hadari, blocked Adel Mostafa's effort but the referee pointed to the spot again immediately afterwards when Awad, who was on the verge of notching home the rebound, was fouled by Yehia again.
Tawfik stepped up this time to convert the penalty and restore parity.
Ismaili once again suffered from the lack of a reliable striker as Ahmed Ali and Mohamed Mohsen Abou-Greisha failed to trouble ENPPI's defense.
They were unlucky not to secure a valuable win though in the dying seconds when Ali's curling free-kick struck the crossbar.