Morsi and others were sentenced to death by hanging
The sentence was initially passed in May, but was confirmed after consultation with Egypt?s highest religious figure, the Grand Mufti.
The death sentences of five other leading members of the Muslim Brotherhood, including its supreme guide Mohammed Badie, were also upheld.
Morsi?s supporters have described the sentence as ?farcical?.
The verdict is subject to appeal. One hundred and one other defendants were also sentenced to death in absentia.
Morsi escaped from Wadi Natroun prison in January 2011 and was accused of colluding with foreign militants in a plot to free Islamists during mass prison breaks.
The 2011 uprising brought an end to Hosni Mubarak?s 30-year rule and Morsi was elected president a year later.
He was deposed by the army in July 2013 following mass street protests against his rule and is already serving a 20-year jail term for ordering the arrest and torture of demonstrators.
Morsi was also sentenced to life imprisonment by the same court on Tuesday for spying on behalf of foreign militant groups, including Hamas.
The judge said that the Muslim Brotherhood had ?collaborated with Palestinian Hamas to infiltrate Egypt?s eastern borders and attack prisons?, state TV reported.
Sixteen other Muslim Brotherhood members were sentenced to death on charges of delivering secret documents abroad between 2005 and 2013.
Only three of the other defendants are in custody, including Muslim Brotherhood leader Khairat al-Shater.
Morsi was overthrown by military chief ? and now president ? Abdul Fattah al-Sisi and was subsequently imprisoned facing various charges.
At the start of Morsi?s first trial in 2013, he shouted from the dock that he was the victim of a ?military coup?.
Since then, Morsi has been forced to sit in soundproof glass cages in courtrooms, which officials say are designed to prevent him disrupting proceedings.