The visitors, who were playing their first competitive match under Emad Soliman, took the lead on six minutes after Abdullah Saied opened the scoring with a header, connecting with a John Owoeri cross.
Owoeri turned scorer to double the Dervishes' advantage three minutes after the interval upon diverting home a cross whipped in by Ahmed Samir Farag.
Ahmed Hassan Farag pulled one back for Gouna five minutes from the hour mark with a header.
But Ndubuisi Godwin hit Ismaili's third in the 90th minute when he converted a one-on-one chance.
Gouna striker Sherif Ashraf scored in injury time with a cross-cum-shot but his strike was not enough for the hosts to salvage a draw.
Ismaili defender Shadi Mohamed was sent off in the dying minutes for cursing his team's keeper Mohamed Sobhi, after the latter accidently collided with a teammate.
Gouna's Farag was also dismissed deep into stoppage time for two bookable offences.
Second-placed Ismail are now on 34 points while Gouna are in 11th spot with 19.
Title holders Ahli will leapfrog Ismaili should they beat Masri in their upcoming league match.