The Whites had to wait till the last 20 minutes to register their victory, thanks to a penalty kick from Ahmed Eid and another fine effort from summer-signing Ahmed Ali.
Masri made their Premier League comeback after being banned following the infamous Port-Said calamity at their home stadium nearly two years back.
Zamalek overcome Al-Shennawi heroics
Zamalek should have taken the lead in the first half if it wasn't for two brilliant stops from ex- keeper Ahmed Al-Shennawi, who was on loan from Masri last season.
However, Zamalek were lucky not to concede a goal near half-time when Masri's international midfielder Hossam Hassan's clever long-range free kick was denied by the crossbar.
In the 70th minute, Egypt winger Eid converted home a penalty following a controversial handball by a Masri defender.
Substitute Ali then managed to ensure the win just one minute after coming off the bench, going one on one with Al-Shennawi before rounding the keeper and slotting into the net to end it 2-0.