The 25-year international striker opened the scoring in the 28th minute before Mohab Said doubled the lead three minutes past the hour mark.
Ayman Hassanein pulled one back for Minya in the 78th minute, but Said killed any hopes of a comeback with a late goal deep in injury time.
Wadi Degla are now third in Group B with 18 points after 11 games and they still have a game in hand.
In Group A, Arab Contractors conceded another disappointed away draw against debutant Ragaa 2-2.
The Marsa Matrouh-based side grabbed the lead through Eslam Fouad after 18 minutes, but Arab Contractors responded with two quick goals from Mahmoud Ezzat, 44, and Ali Fathi, 50, to overturn their deficit.
However, Tamer Moheb gave them a huge blow after hitting the equaliser just a few seconds before the final whistle.
Arab Contractors – who had an amazing season start – have been struggling lately as they have only won once in their previous six games.
They are now third in their group with 21 points after 12 matches.