63-year-old Morsi, who appeared in the Cairo Criminal Court in a caged dock wearing the blue uniform of convicts, was charged in the case with over 100 co-defendants, including Brotherhood leaders Badie, Mohamed Saad El-Katatni, Essam El-Erian, Mohamed El-Beltagy and Safwat Hegaz.
The court sentenced Morsi, Muslim Brotherhood Supreme Guide Badie and 104 Muslim Brotherhood leaders to death in the case.
Today's capital punishment ruling against Morsi makes him the first president in Egypt's history to face the possibility of death by hanging if court ratifies its initial decision on June 2 or he loses his projected appeal.
The verdict in the case was referred to the Grand Mufti, who according to the Egyptian law must review all death sentences, however, his decision is not binding.
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Many of those sentenced were tried in absentia.
They were accused of damaging, setting fire to prison buildings, murder, attempted murder and looting prison weapons depots while allowing prisoners to break out of jail.
The court also sentenced 16 Muslim Brotherhood leaders including Khyrat el-Shater, the deputy of the Muslim Brotherhood supreme guide, to death in a separate espionage case.
Morsi is also an accused in the espionage case along with 35 others but the court will pronounce the verdicts for Morsi and the remaining defendants in that trial at a later date.
In the espionage case, the Islamists are charged with conspiring with foreign powers -- including the Palestinian Islamist group Hamas, Lebanon's Hizbollah and Iran's Revolutionary Guard -- to destabilise Egypt. The defendants are also accused of funding terrorism and disclosing national security.
Morsi had ruled for only a year before mass protests prompted the military to overthrow him in July 2013.
Morsi is also being tried over insulting the judiciary, spying and handing documents of national security importance to Qatari intelligence through the Al-Jazeera news channel.