Security officials, speaking on condition of anonymity because they weren't authorized to brief reporters, said police arrested 29 people.
A statement from the health ministry early Sunday said one person was killed and nine were injured in the clashes.
The dispersal of protesters contrasted with the jubilant well-wishers who greeted Mubarak after the decision when he returned to his temporary home at a Nile-side military hospital. He later triumphantly waved back to supporters from his hospital window.
A television interviewer reached him by telephone, asking whether he had ordered the killing.
"I did not do anything at all," replied Mubarak, who was convicted and sentenced to life in prison in 2012 on charges related to the killing of protesters. The verdict was overturned on appeal the following year.
That question likely won't be answered in Egypt's courts. Already, nearly 170 police officers and security officials put on trial in connection to the killings have either been acquitted for lack of evidence or were found to have acted in self-defense. Some received short, suspended sentences.
The Mubarak trial, however, was concerned only with the killing of 239 protesters whose names were cited in charge documents, not the nearly 900 killed in total during the 18 days of the revolt.
Saturday's ruling marks another major setback for the young activists who led the 2011 Egyptian uprising, many of whom are now in prison or have withdrawn from politics. It likely will reinforce the perception that Mubarak's autocratic state remains in place, albeit led by el-Sissi, the former military chief who later led the overthrow of Islamist President Mohammed Morsi in 2013.
It concludes Mubarak's retrial along with his two sons, his security chief Habib el-Adly and six top security commanders, who were all acquitted. Also acquitted was wealthy businessman Hussein Salem, a longtime Mubarak friend tried in absentia.
Hossam Bahgat, a prominent human rights advocate, said Saturday's verdict would be used by the government to signal the end of the upheavals associated with the 2011 revolt.
"The regime's message: It's time to look forward, time to move on, time to focus on building the nation. But I doubt this will work. It will deepen the grievance and feeling of injustice felt by many young people," Bahgat said by telephone from New York.
Mubarak was also acquitted of corruption charges that he faced along with his sons Alaa and Gamal — his one-time heir apparent — over the statute of limitations in the case running out. The case involves their purchase from Salem of luxury villas in a Red Sea resort at a vastly discounted price, something that the prosecution had said amounted to bribery. The two sons face a separate trial on charges of insider trading.
All the rulings can be appealed.
It was not immediately clear whether Mubarak would now walk free since he is serving a three-year jail term for separate corruption charges he was convicted of in May. He has been in detention since April 2011, but it is unclear if the past 3 1/2 years will be treated as time served.
Al-Rashidi, the judge, said the dismissal of the charges did not absolve Mubarak of the corruption and "feebleness" of the latter years of his 29-year rule. The judge praised the 2011 uprising, saying that its goals — freedom, bread and social justice — were legitimate.
He also said Mubarak, like any other human, erred at times and suggested that his old age should have spared him a criminal trial.
"To rule for or against him after he has become old will be left to history and the Judge of Judges, ... (God), who will question him about his rule," the judge said.
From the Associated Press. AP writers Sarah El Deeb and Merrit Kennedy contributed to this report.