The ruling puts an end to a protracted transfer saga that involved Zamalek, Ittihad and Egyptian champions Ahli.
Geddo signed a deal to join Zamalek before extending his contract with Alexandria-based club Ittihad, which was due to expire at the end of last season.
He eventually joined Ahli in the close season to incur the wrath of Zamalek, who lodged a complaint with the Egyptian FA but the ruling body's verdict did not satisfy them.
"A decision has been taken unanimously to fine Geddo EGP 2.2 million," EFA board member Magdi Abdul-Ghani said on Sunday, few hours before Ahli take on Ismaili in the African Champions League.
"Zamalek will be given an EGP 1.2 million because they paid that amount to Geddo.
"Geddo will also have to pay an additional EGP 1 million to the EFA as a penalty for signing for two clubs at the same time.
"The EFA regulations state that a player who signs for two clubs must be fined. The punishments in such cases do not include any bans though."
Zamalek wanted Geddo, who was the Nations Cup's top scorer with five goals in Egypt's triumphant campaign in Angola, to be suspended.
They are likely to take the matter to the Court of Arbitration for Sport (CAS).
"The EFA proved once again that they are biased. They take the decisions which serve one color," Zamalek vice-president Raouf Gasser said in reference to Ahli.
"But we will pursue our rights, we will file another complaint to CAS."
Zamalek's relationship with the EFA is already frosty as both sides clashed several times last season.
The White Knights believe Ahli, the most popular team in Egypt, are always favored by the EFA.