Mokhtar Mokhtar's side were joint leaders with Ahli prior to the game after claiming seven points from three matches.
However, a goal from attacking midfielder Ahmed Omran seven minutes past the hour mark sank them and handed Gouna their first victory of the season.
The win will boost a Gouna side who lost two influential midfielders to long-term injuries as playmaker Amr Samaka and versatile midfielder Wael Riad ruptured cruciate ligaments in their knees.
Petrojet are now three points behind defending champions and leaders Ahli, who produced a ruthless attacking display to defeat Gaish 4-2.
Police Union moved into second place ahead of Petrojet on goal difference, thanks to a 2-1 win over Asyut Petroleum.
Ahmed Duiedar put them in front with a sixth-minute penalty and Nigerian striker Minusu Buba extended their advantage on 26 minutes.
Asyut's Mashour Ahmed pulled one back seven minutes before the interval but Police held onto their lead to secure a precious win.
Ismaili ended their winless run with a 1-0 home victory over Arab Contractors.
Ahmed Ali struck home on in the 54th minute to give the Dervishes their first win under new coach Emad Soliman, who replaced Serbian Nebojsa Vuckovic.
Ismaili, who finished runners-up to champions Ahli last season, have five points from three matches.