He was acquitted by an Egyptian military court and will be released Tuesday, said attorney Nizar Ghorab.
Mohamed al-Zawahiri was imprisoned in 1999 after being detained and extradited from the United Arab Emirates on allegations that he was linked to the 1981 assassination of Egyptian President Anwar Sadat. Al-Zawahiri was acquitted on the assassination charges but later was accused of conspiring against the Egyptian government.
He was sentenced to death, but then appealed the ruling.
Last year, Egypt's interim government released him along with scores of other political prisoners after a general pardon was issued by the Supreme Council of the Armed Forces, which ruled the country after the ouster of President Hosni Mubarak. But al-Zawahiri was arrested again shortly after.
Ahmed al-Zawahiri, nephew of Mohamed al-Zawahiri, told CNN that after the release last year, security forces stormed his uncle's home, beat him up and rearrested him for no apparent reason.
"It was a day after my uncle spoke to a local paper and spoke of the torture he endured inside prison for years," Ahmed al-Zawahiri told CNN.
"He paid a high price for being Ayman's brother and he has denounced any sort of violent ideologies now that his main enemy, the Mubarak regime, has been removed," the nephew added.
"Zawahiri has been tortured for years by Mubarak's state security officers because he is the brother of Ayman Zawahiri," Ghorab said.
Mohamed Al-Zawahiri is a member of the Egyptian Islamic Jihad, of which his brother was once a leader. The United States describes the group as a terrorist organization that merged with al Qaeda in 2001. Its "primary goals are to overthrow the Egyptian government and replace it with an Islamic state and attack U.S. and Israeli interest in Egypt and abroad," the U.S. State Department once said.
Five other Islamists charged with similar crimes were acquitted along with Al-Zawahiri, said Ghorab.
They are Abdel Aziz al-Jamal, Alaa Sarhan, Sayed Imam, Murgan Mustapha Salem and Mohamed Islamboli, the brother of the executed Islamist who killed Sadat, the attorney said.
