Both players sustained hamstring injuries, with El-Shennawi being unable to complete the match against Ceramica Cleopatra and being replaced six minutes before halftime.
Ibrahim also suffered a hamstring strain during the same game.
They will undergo scans to determine the extent of their injuries and their availability for the final.
Ahly are looking to secure their 14th Egyptian Super Cup title and their third consecutive victory in the competition.
The final will be held in the United Arab Emirates, with four teams participating instead of the usual two.
Ahly advanced to the final by defeating Ceramica Cleopatra, while Modern Future FC secured their place in the final after a thrilling penalty shootout victory over Pyramids FC, which ended with a score of 14-13.
Ceramica Cleopatra and Pyramids FC, will face each other in a separate match on Thursday.
This edition of the Super Cup will feature four teams instead of the usual two.
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