Judge Mahmud Kamel al-Rashidi also acquitted Mubarak of corruption charges for exporting gas to Israel.
The court ruled that Mubarak’s seven former security commanders, including his former interior minister Habib al-Adly, were “innocent” in the killing of anti-government protesters during the 2011 revolution.
The 86-year-old, dressed in his trademark shades and wearing the blue clothes of a convict, was wheeled into the caged dock on an upright stretcher.
His two sons were also acquitted from all corruption charges.
Mubarak and his co-defendants were found guilty in June 2012 and sentenced to life imprisonment.
The initial verdict was appealed successfully and a retrial began in April 2013.
He is serving a separate three-year prison term for embezzlement of public funds.