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 Shia Hezbollah, and Iran.
Tuesday's verdicts can be appealed.
More: Egyptian court sentenced former President Mohamed Morsi to 25 years in prison for spying and conspiring with foreign groups.
A total of 17 were given life sentences including Muslim Brotherhood leader Khairat el-Shater and two others to death in the same case.
Death sentences were also handed to 13 other defendants in absentia.
Morsi had been sentenced to death on May 17 for a mass prison break in 2011, prompting immediate condemnations from rights groups and world leaders.
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| Egyptian authorities have banned Morsi's Muslim Brotherhood since his overthrow and arrested thousands of his supporters. |
The court had ruled that the sentencing of Morsi and other defendents would be referred to the grand mufti, the highest religious authority in Egypt, for confirmation before the final verdict.
In April, a court sentenced Morsi and 12 other defendants to 20 years in prison for ordering the arrest and torture of protesters in clashes outside the presidential palace in December 2012.
