Islam Atteya scored the winner against URA (Photo: Masry twitter account)
Following a scoreless away-leg draw last Saturday, Islam Atteya's sublime curler from outside the box in the 37th minute proved to be the decider and gave new coach Moine Chaabani a winning home debut.
Masry could have put the game beyond doubt in the first half but Austin Amutu and Mohamed Antar lacked the cutting edge in the final third.
The hosts took their foot off the gas pedal in the second half, allowing the Ugandans to grow in confidence and mount some threats.
Keeper Ahmed Massoud made some fine stops to block close-range efforts from Mukuwala Steven, Kagimu Shafik and Ojera Joackim.
Masry will face one of the teams who are eliminated from the African Champions League second preliminary round for a place in the Confederation Cup group stage.
(For more sports news and updates, follow Ahram Online Sports on Twitter at @AO_Sports and on Facebook at AhramOnlineSports.)