Rival fans invaded the pitch and fought after Al Masry recorded a surprise 3-1 win over Al-Ahly.
Reports say at least 74 people have died in the unrest while up to a thousand others are injured after the violence quickly spread.
The Egyptian federation statement: "The Egyptian federation has decided to stop the football leagues in all four divisions for an indefinite period after the violence that occurred in the game between Al Masry and Al-Ahly, which represented a tragic shock to the centre of sport in general and the football family in particular.
"The federation has announced that Egyptian football will be in mourning for three days for the souls of those who have fallen victim to the violence that occurred in the wake of the Al Masry-Al-Ahly match."
FIFA president Sepp Blatter: "I am very shocked and saddened to learn this evening that a large number of football supporters have died or been injured following a match in Port Said, Egypt.
"My thoughts are with the families of those who have lost their lives this evening.
"This is a black day for football. Such a catastrophic situation is unimaginable and should not happen."