The 63-year-old former president was, however, acquitted of murder charges in the killing outside the presidential palace in December, 2012 that would have seen him face the death penalty.
Besides Morsi, the criminal court sentenced 12 other top Muslim Brotherhood leaders, including senior figures Mohamed el-Beltagy and Essam el-Erian, to 20 years in jail as they stood in a soundproof glass cage inside a makeshift courtroom at the national police academy here.
The conviction and no strong reactions from the party show the dramatic downfall of Egypt's once-powerful Muslim Brotherhood and its leader.
Morsi - who was deposed by the military in July, 2013 after thousands of people took to the streets demanding his removal - and 13 others were charged with killing protesters, possessing weapons, and inciting violence in the dispersal of the peaceful sit-in in front of the presidential palace.
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The judge dropped murder charges against all 14 defendants and said the sentence was linked to the "show of force" and unlawful detention associated with the case.
Morsi is currently in prison over other cases, including espionage, escaping from prison during the January 25 Revolution in 2011, insulting the judiciary and spying and handing documents of national security importance to Qatari intelligence through the Qatar-based Al-Jazeera news channel.
The incident took place in December 2012, during Morsi's presidency, after opposition forces rallied in front of the Ittihadeya presidential palace to hold a sit-in to peacefully protest his decree in which he ordered that the president shall be immune from any judicial oversight.
Four of the 12 defendants in the case are being tried in absentia.
Authorities have banned the Muslim Brotherhood party and arrested thousands of Morsi's supporters.
Amnesty International condemned the trial, terming it as a "sham" and called for Morsi's release.