Morsi was sentenced to death along with five other Muslim Brotherhood leaders, including the supreme leader Mohamed Badie.
Last month, a court upheld a 20-year jail sentence for Morsi over the killing of protesters in December 2012.
Mursi, democratically elected after the revolution, was overthrown in mid-2013 by then-general Abdel Fattah al-Sisi, now the president, following mass protests against his rule, and immediately arrested.
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Tuesday's court decision means the former president - who has remained in prison since Egypt's 2013 military coup - no longer faces the threat of execution.
Egypt's ousted President Mohamed Morsi, wearing a red uniform, stands behind bars during his trial. Over the jailbreak, the court claimed that Morsi and other Muslim Brotherhood members unlawfully left the prison. "I am optimistic but I also don't expect much from politicized judiciary", he said.
A total of 93 others were sentenced to death in absentia. Even so, observers widely believe that executing top leaders like Morsi could lead to a new surge of violence. Their sentences were also overturned.
Islamist militants have waged an insurgency that has killed hundreds of policemen and soldiers since Morsi's ouster.
In September, militants set off a vehicle bomb as the country's deputy state prosecutor was passing by.
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