Egyptian security forces shot one person dead late on Saturday, either with live ammunition or birdshot, as they moved in and cleared the protesters off the streets.
Dozens more demonstrators, some hurling rocks, were injured as teargas and birdshot were fired near Cairo's iconic Tahrir Square.
Around 2,000 people had gathered to protest the decision to dismiss murder charges against Mubarak, his interior minister and six aides over the deaths of nearly 900 demonstrators in the 18-day uprising that toppled the former leader.
Mubarak and his sons, Alaa and Gamal, were also cleared by Chief Judge Mahmoud Kamel al-Rashidi of corruption charges related to gas exports to Israel.
The judge said too much time had elapsed since the alleged crimes took place for the court to rule on the matter.
Reacting to the verdict, Mubarak denied responsibility for the protesters' deaths, in a phone call to a local television station.
"I felt I did nothing wrong at all. I was waiting to find out what they will come up with this time. It was an innocent verdict. I did nothing wrong at all," he said.
"But, we cannot change destiny. When I heard the previous ruling I laughed. This time I was just waiting. I felt indifferent. It is all in the hands of God."
Mubarak, 86, did not walk free after Saturday's verdicts. He was found guilty in May in another case, related to the theft of public funds, and he has been serving that three-year sentence, under house arrest for medical reasons, in an army hospital in a posh Cairo suburb, Al Jazeera reported.