Ahmed Sedik gave the Dervishes the lead on 56 minutes but Gamal Hamza hit an equalizer on the hour mark.
Ahmed Samir Farag, who hit a brace against ENPPI last week, rose to prominence once again and netted the winner in the 69th minute.
Ismaili are now keeping pace with Gaish on top of the league table with nine points. Both sides have won their first three matches.
The coastal outfit's duo Ahmed Ali and Amr Al-Sulaya were sidelined by head coach Mark Wotte, who wanted to rest them for the Champions League trip to Nigeria's heartland.
Gouna were superior in the first half.
They carved out a number of scoring chances that could have resulted in goals against the home side if it wasn't for goalie Mohamed Sobhi.
The second half was much more eventful than the first.
Sedik hit the opener with a powerful shot but Ismaili's slender lead was soon canceled out when Hamza converted a penalty kick.
Fully-fit Farag gifted Ismaili all three points when he scored with a well-placed shot.
The match's goals