With the match ending in a goalless draw, the outcome was determined by a marathon penalty shootout, as both teams set a new record with a total of 17 shots.
Modern Future will face the winner of the second semifinal clash between Ahly and Ceramica Cleopatra, scheduled to take place later on Monday.
The final of the revamped Egyptian Super Cup will be held on Thursday.
Modern Future was forced to make two substitutions due to injuries, with Mohamed Rabia and Bello Martins coming on for Mohamed Abdel-Salam and Mohamed Farouk, respectively.
The first half witnessed few scoring opportunities from both teams, with Pyramids FC launching minor attacks and Modern Future FC displaying a solid defense.
Pyramids FC started the second half with renewed motivation, pushing for victory.
Just eight minutes after the break, winger Abdallah El-Said came close to scoring with a low strike near the goal.
In the 77th minute, substitute striker Ahmed Atef nearly gave Modern Future FC the lead with a powerful strike from inside the area, but Pyramids FC goalkeeper Ahmed Mayhoub made a remarkable save to deny him.
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