He will undergo surgery this week after a crunching tackle from Thabo Nthethe in the Group B match in Cairo which the South African champions won 2-1.
"The initial medical tests showed that Ibrahim has broken his fibula and dislocated his ankle," team doctor Walid Abdel-Rahman told reporters in Cairo.
"He is expected to be out of action for three months."
It means Ibrahim misses Zamalek's remaining games in the Egypt Cup and Champions League, as well as the start of the new season.
Zamalek travel to Pretoria next week to take Sundowns.