The court also cleared Mubarak, his sons and a business associate on corruption charges, but he will remain in prison because he is serving a three-year sentence in a separate corruption case.
Only history and God should be called on to issue judgement on someone who served as vice president and then president of Egypt for over 30 years, Judge Mahmoud al-Rasheedi says.
Egyptian court on Saturday acquitted all seven security commanders charged with murder alongside ousted president Hosni Mubarak over the deaths of protesters during a 2011 uprising.
Judge Mahmud Kamel al-Rashidi said the commanders, including Mubarak's former interior minister Habib al-Adly, were "innocent".
About 800 people were killed during the 18-day uprising that unseated Mubarak, in which protesters clashed with police across the country and torched police stations.