Mubarak and his interior minister, Habib al-Adly, were convicted and sentenced to life in prison in 2012 on charges of failing to protect the lives of demonstrators, but another court threw out the verdict two years later, citing technical flaws in the prosecution.
The ailing 88-year-old Mubarak was flown by helicopter to the courtroom from the Cairo military hospital where he has resided for most of the last six years, and where he served a three-year sentence for corruption charges in a separate case.
He sat in a wheelchair in the defendant's cage during the hearing. When the charges against him were read out, he responded: "It did not happen." Later he exchanged smiles and winks with a dozen or so supporters in the courtroom, including his two sons — Gamal, who was once groomed to succeed him, and Alaa.
Mubarak does not face any other charges and is technically free to go, but it was unclear whether he would leave the hospital, where he has been under informal house arrest in recent years.
Mubarak and figures from his government were widely vilified in the months after the uprising, but many have gradually returned to public life since 2013, when the military overthrew his freely elected successor, the Islamist Mohammed Morsi, after a divisive year in power.
Since then, the government has waged a heavy crackdown on dissent, jailing thousands of people, mostly Islamists but also scores of secular and liberal activists, including some of those who led the 2011 uprising. The government has also banned all unauthorized demonstrations.
Negad Borai, a prominent human rights lawyer, conceded that there was not enough evidence for Mubarak to have been found guilty of the specific charges he faced, but said he still blamed Mubarak's long autocratic rule for Egypt's woes.
"Mubarak is now technically an innocent, but he killed the future of a country, both directly and indirectly. The question now is how we move forward as a nation," he said.
International and local rights groups say the freedoms won in the 2011 uprising have been lost since then, and that the security services today are even more brutal and repressive than under Mubarak.
President Abdel-Fattah el-Sissi, who as military chief led Morsi's overthrow, has defended the government's actions, saying they are needed to restore political and economic stability after years of unrest.
After a meeting with visiting German Chancellor Angela Merkel on Thursday, el-Sissi said his government is trying to strike a "balance between human rights and security measures." He suggested that Germany would have taken similar action if it faced "the same threats and attacks."
An Islamic State affiliate based in the northern Sinai Peninsula has carried out scores of attacks in recent years, mainly targeting Egyptian security forces. A recent wave of attacks on Christians in northern Sinai led hundreds to flee.