A lower court in June condemned to death 183 Islamists, including the 33, for the alleged murder of two policemen and attempted murder of five others in the southern province of Minya on August 14, 2013.
The defendants were found guilty of committing the murders on the same day that police killed hundreds of Morsi backers in Cairo clashes.
The June verdict came after a speedy mass trial and sparked an international outcry, with the United Nations saying such mass verdicts were "unprecedented in recent history".
On Tuesday, the Court of Cassation overturned the death sentences of the 33 Islamists and life terms of three others, and ordered their retrial, the official MENA news agency and defence lawyer Mohammed Tosson said.
The 36 defendants were in custody and had appealed against the lower court's verdict, said Ossama El-Helw, another defence lawyer.
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Other co-defendants sentenced to death had been tried in absentia as they are on the run, and automatically face a retrial if they surrender.
Among those tried in absentia and sentenced to death last June was Mohamed Badie, who heads Morsi's Muslim Brotherhood movement, although he was in prison at the time of the trial.
Badie will also be retried.
In January, the appeals court ordered a retrial of another group of 152 Islamists, including 37 sentenced to death, in a similar case in Minya.
Critics accuse President Abdel Fattah al-Sisi's regime of using the judiciary as a tool to repress its opponents.
They say Sisi has installed a regime that is more repressive than that of longtime president Hosni Mubarak, who was ousted in a 2011 popular uprising.
Since Sisi, who was then army chief, ousted Morsi in July 2013, a government crackdown has left more than 1,400 people dead, thousands jailed and hundreds sentenced to death.