كتب : وكالات
The court overruled their initial order to the National Sports Council (NSC) to sack Zaher, who was allegedly ineligible to run for the post in 2008 due to criminal record.
The NSC is expected to issue the reappointment decision soon.
Egypt won the African Cup of Nations three times in a row in 2006, 2008 and 2010 during Zaher's two spells at the helm.
He was also praised for generating income for Egyptian clubs through selling the league's broadcasting rights to several TV networks.
However, critics sharpened the knives for him during the past year after many disputes erupted in domestic football.
Zaher would have stepped down as the EFA president anyway in 2011 because regulations would not have allowed him to remain in his post for a third successive stint.