Defensive blunders by the visitors proved costly as Samir Fekri and Amr El Saadawi scored in the 14th and 34th minute respectively to exploit on some poor defending.
Substitute Fakhreddine Ben Youssef sealed the win in the 88th minute with a cross from fellow substitute Ahmed Eid.
Masry now has 20 points from 11 games, one point behind third-placed Pyramids. Baladeyet El-Mahalla remains in 12th place with 13 points.
Dakhleya and Pharco remain in the relegation zone after a 1-1 draw.
Walid Ali Farag put Pharco ahead in the first half, but Allan Kyambadde equalized for Dakhleya in the second half.
Dakhleya has eight points from 12 games, while Pharco has six points from 11 games.
Ceramica Cleopatra salvaged a 1-1 draw against Gouna thanks to a stoppage-time goal by Marwan Osman.
Ayman Saad had given Gouna the lead in the 58th minute.
The result leaves both teams on 15 points, with Ceramica Cleopatra in eighth place and Gouna in ninth on goal difference.
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