The Egyptian side lifted the trophy after a 2-0 victory over Orlando Pirates secured a 3-1 aggregate victory, with Zaher netting his side's second in the 78th minute.
However, the attacker celebrated by demonstrating the Rabaa symbol - a four-finger salute commemorating a sit-in protest by supporters of ousted president Mohammed Morsi that was violently dispersed by security forces, leading to the deaths of hundreds of people.
With the club reportedly set to exclude Zaher from December's FIFA Club World Cup in Morocco, Zaher is said to be penning an apology to the Egyptian Football Association and supporters.
"Ahmed Abdel Zaher feels that he made a mistake and is currently drafting an apology to National Board of Directors and the fans of different religious and political affiliations," read a statement on Al Ahly's website.
Zaher was quoted by Egyptian football website FilGoal earlier in the week, saying: "Yes, I raised the sign of Rabaa.
"But I didn't mean political excitement to any one side or fan.
"All I meant to do was to remember the dead, whether in Rabaa, any other citizen and even policemen.''
Kung Fu fighter Mohammed Youssef was banned from competing for two years after displaying the same symbol at a medal ceremony last month.
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