The Ismailia criminal court on Tuesday sentenced nine of the defendants to 15 years in prison and 43 others to 10 years. Another 22 were sentenced to three to seven years, and 14 were acquitted. Nearly half of the defendants were tried in absentia.
The defendants were accused of burning police vehicles and attacking a coffee shop. The violence came in response to the dispersal of two mass sit-ins in Cairo in 2013, in which security forces up to a thousand Muslim Brotherhood supporters.
The Muslim Brotherhood won a series of free elections following Egypt's 2011 uprising but was branded a terrorist group after the military overthrew the country's first democratically elected president in 2013.
The Court of Cassation rejected appeals against a ruling passed by a lower court in June last year.
The defendants were accused of training militants and plotting violence in the country, the source said.
The list includes leading Muslim Brotherhood figures, many of whom fled Egypt following the military ouster of Islamist president Mohamed Morsi.
Hundreds have been added to Egypt's terrorism list in recent years, including Morsi himself, which activists say is used to intimidate opponents of the regime.
Since the arrival of President Abdel Fattah al-Sisi to power after the military coup in 2013, Egyptian security forces have launched a wholesale crackdown on dissent and political activist as well as banning and dissolving NGOs.
According to critics, Sisi's rule over Egypt has seen the worst crackdown on freedom of expression in the country's recent history.