“The Court has found the defendant innocent,” Judge Ahmed Abdel Qawi said after an all-day hearing.
The court also rejected demands by lawyers of the victims to reopen civil suits, leaving no remaining option for appeal or retrial.
After three decades of authoritarian rule, Mubarak was ousted in a popular uprising in February 2011. Following the revolt, he was brought before court for several cases concerning corruption and death of demonstrators in the uprising.
Mubarak was first convicted on the charges in 2014, two years after he was handed life sentence for complicity in the murder of 800 anti-regime protesters during the 2011 uprising.
In May 2014, Mubarak was also found guilty of embezzling public funds for the modernization of the presidential palace. His sons Gamal and Alaa were prosecuted on the same charges. Mubarak was sentenced to three years in prison and his sons received four years each.
The former long-time Egyptian ruler has long maintained his innocence in the case and has said history would judge him a patriot who served his country selflessly.
The Thursday ruling means Mubarak is expected to be freed.