The Court of Cassation also cancelled life sentences for 21 others in the same case.
Five co-defendants, including Badie, who also received death sentences in June 2015, will be retried too.
Morsi and other Brotherhood leaders were sentenced to death in June 2015 for escaping from Wadi al-Natroun prison, damaging and setting fire to prison buildings, murder charges, looting weapons and allowing prisoners to break out of jails during the January 2011 revolution.
In another case, Egypt's first freely elected civilian president was found guilty of stealing documents relating to national security and handing them to Qatar.
Morsi came to power after Egypt's long-time President Hosni Mubarak was overthrown in 2011.
He was toppled by the current President Abdel Fattah al-Sisi following mass street protests.
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