The court had initially sentenced Morsi and more than 100 other defendants to death last month.
Tuesday’s ruling comes after the court consulted Egypt’s grand mufti, the government interpreter of Islamic law who plays an advisory role.
Earlier on Tuesday, the same court sentenced Morsi, the country’s first democratically elected president, to life in prison on charges of spying for the Palestinian Hamas movement, Lebanon’s Shiite Hezbollah, and Iran.
Tuesday’s verdicts can be appealed.
Then army chief and now President Abdel Fattah al-Sisi ousted Morsi on July 3, 2013, and since then has overseen a sweeping crackdown against his supporters.
The crackdown has left hundreds of Islamists dead and thousands jailed.
Hundreds have been sentenced to death after speedy mass trials described by the United Nations as “unprecedented in recent history”.
In the jailbreak trial, exiled Egyptian-born cleric Yusuf al-Qaradawi, who commands huge influence through his appearances on Al-Jazeera television from his base in Qatar, was also condemned to death in absentia.