Playmaker Mohamed Ibrahim scored the winner after 30 minutes, heading home at the far post after a mix-up between defender Ali Gabr and keeper Sherif Ekramy.
The game marked the first appearance of Greek coach Gonias, who was named as the team's new boss for a second stint on Sunday.
His appointment came hours after the club were eliminated from the African Confederation Cup quarters following a 2-0 aggregate loss to DR Congo giants TP Mazembe.
Gonias replaced Ehab Galal, who took over as Egypt's national team coach last month.
Pyramids FC are third in the league table with 29 points, six points behind leaders Zamalek who played a game more.
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