Cairo giants Zamalek claimed a 1-0 victory at Fayoum courtesy of a header from Ahmed Gaafar eight minutes past the hour mark but the match was halted for several minutes afterwards following a bizarre incident.
TV cameras caught Zamalek fans hurling stones at people standing in the balconies of nearby buildings. Security forces eventually intervened to end the matter.
Fayoum fans also sang offensive chants against Zamalek and their coach Hossam Hassan.
"Zamalek and Fayoum are fined EGP 10,000 for throwing stones and hurling insults at each other," the EFA said in a statement on their official website.
Hassan has earlier called on the EFA to punish Fayoum fans, whom he believes were the supporters of Zamalek's arch-rivals Ahli.
Gaafar made a 'shush' gesture toward the home fans after heading home the winner.
Ahli and Zamalek meet in the Egyptian Cup round of 16 on Wednesday for their third Cairo derby clash this season.