The hackers posted the Egyptian flag on the homepage as well as the Red Devils' logo and slogan 'Ahli are above all'.
They also left a message in French which reads: "The site has been hacked by Egyptian hackers.
"The keyboard is my weapon and I will use it to defend all Egyptians' rights."
They also accused the referee who officiated the match of being biased.
The Red Devils have suffered their first defeat in Algeria since 1988 after losing 1-0 at JS Kabylie in a clash that witnessed an ugly brawl towards the end on Sunday.
Ahli appeared to have snatched a valuable equalizer when substitute Mohamed Shawky struck home with four minutes remaining.
The goal, however, was correctly ruled out for offside but a free-for-all erupted afterwards between Ahli's players and the stadium's security personnel.
Punches and kicks flew from both sides for no apparent reason, with some Kabylie players involved in the unfortunate incident.
The match, which was preceded by an attack on Ahli's bus on Saturday , was halted for around eight minutes.
The Cairo side's bus was stoned once again after the match, to further inflame feelings of Ahli's supporters.
The second match will be held in Cairo on August 29th.