The court upheld 21 death sentences and handed down prison terms to other defendants over the violence, which claimed 74 lives.
Most victims were supporters of a Cairo team, and fans there criticized the sentencing for not going far enough.
In Port Said, fans of the local team accused the court of unfairness.
Many people believe police in the city stood by during the rioting in revenge for the role of football supporters in the unrest which toppled Hosni Mubarak as president a year before. Police deny the accusation.
Ahead of Saturday’s sentencing, the army assumed policing in Port Said, which saw fresh unrest last week.
Police in at least 10 of Egypt’s 29 provinces have been holding an unprecedented strike in protest at being used by the government of Islamist President Mohamed Morsi to confront protesters.
Fans had surged through the streets to attend a rally at their stadium, and a police club and the Egyptian football federation building were set alight in the chaos.
Both buildings are close to the team’s stadium and a senior security official was quoted as saying by AFP news agency that some fans had stormed the club and torched it.
Confirming the capital punishment sentences, Judge Sobhi Abdel-Maguid specified “the death penalty by hanging”.
In addition:
The court’s verdicts, broadcast live on TV, were initially cheered by fans of Cairo’s al-Ahly team, who are known as the Ultras.
“First we were happy when we heard the 21 death sentences,” one fan told AFP news agency.
“We were cheering and didn’t hear the rest of the verdict. Then we were very angry.”
Two demonstrators died on Saturday in Cairo in clashes with police, said the head of the city’s ambulance service. One was killed following inhalation of tear gas and the second by birdshot.
The clashes, near Tahrir Square, were originally thought to be connected to the football riot trial, but it later transpired to be unrelated. Unrest in the area flared up last week when police tried to open Tahrir Square to traffic.
In Port Said, fans of local team al-Masri were already angry that all of those sentenced to death were supporters of the team.
Two senior police officers were jailed but seven other security officials were acquitted, fuelling local resentment.
Some demonstrators tried to block the Suez Canal by untying speedboats and setting them adrift while others sought to interrupt car ferry traffic.
Military police recovered five of the speedboats and brought them back to shore, but two were still drifting, one witness told Reuters news agency.
However, the canal was protected by troops backed by tanks, and military helicopters hovered above the crowd.
Before Saturday, the canal, a global shipping route, was considered off-limits by protesters, correspondents say.
At least seven people – civilians and security officials – died earlier this week in unrest in the city.
The original death sentences imposed on the 21 defendants in January sparked a local revolt.
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