Rival fans flooded onto the pitch, hurling stones and sticks at each other and sparking a stampede.
One thousand other people were injured, the Health Ministry said.
A medical official said some of the dead were security officers.
Egypt's state prosecutor has ordered an immediate investigation into the causes of the deaths.
Witnesses say most appeared to have occurred in a stampede after fans of the home team, Al-Masry, stormed on to the field following a rare 3-1 win against Al-Ahly, Egypt's top team.
They then chased players and fans from Al-Ahly.
The clashes happened in the Mediterranean port city of Port Said.
The Egyptian Football Federation have announced an indefinite suspension of all leagues in the country following the violent clashes in Port Said on Wednesday night that left dozens dead.
The Egyptian federation issued two statements on Wednesday night, announcing a period of mourning and a suspension of football in the country.
"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," one statement said.
The other added: "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 issued a statement to express his sympathy for the families of the victims.
"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," the statement said.
"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."