The court will give its final sentence against another 13 accused with the same charges in November 25.
On October 22, 2016, the same appeals court had confirmed a 20-year prison sentence against Morsi on charges of violence and murder in 2012, when clashes erupted outside a presidential palace between his supporters and opponents, which killed up to 10 people.
A life sentence in Egypt amounts to 25 years in prison, and the court's rulings can not be appealed.
The court also confirmed death sentences against three defendants in the same case.
But it upheld a life sentence - 25 years in prison in Egypt - on the charge of leading an illegal organisation, his lawyer Abdel Moneim Abdel Maqsud told AFP.
The defendants were accused of sneaking classified documents about the armed forces that harm the national security to Qatar.
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He came to power after Egypt's long-time president Hosni Mubarak was toppled in an uprising in 2011.
Morsi, Egypt's first democratically elected president, was overthrown by the military in July 2013 following mass protests against his one-year rule.
Morsi was immediately arrested after the coup and Sisi has been the president of the country since 2013.
The final decision of the court will be announced on November 25 which involves 20 defendants.
Charges also include possessing weapons, inciting violence and participating in the slaughtering of 21 Egyptian Coptic Christian workers in Libya in 2015.
Qatar is now embroiled in a crisis with Egypt, Saudi Arabia and the United Arab Emirates which are boycotting the small Gulf emirate for its support for the Brotherhood, among other accusations.