Mohamed Ibrahim, known as "Mohamed el-Sunni," had initially been sentenced in absentia to death in connection with the killings, but eventually turned himself in and was granted a retrial.
In that trial he was handed a five-year sentence, which he appealed.
He was accused of participating in the killing of 18 protesters on January 28, 2011, when thousands of people attacked and torched police installations, prompting the hated interior ministry's forces to withdraw from the streets.
January 28 was dubbed the Day of Rage and seen as the turning point in the protests against longtime president Mubarak.
Details were not available on the reasoning for the court's decision, but Gamal Eid, head of the Arabic Network for Human Rights, denounced what he said was double standards in the courts.
"There is no political will to punish the criminals," Eid told AFP.
"The great majority of police officers accused of killing protesters have been acquitted while the youth are now being arrested for protesting or raising the rabaa sign," Eid said.
He was referring to the four-fingered salute used by Islamist protesters to remember the deadly dispersal by security forces of the Rabaa al-Adawiya sit-in in Cairo that left at least 600 dead in August.
The sit-in was calling for Morsi's reinstatement, ousted by the army the previous month.
Since Morsi's ouster, authorities have been waging a deadly crackdown on his supporters that has left more than 1,400 people dead according to Amnesty international.
The government also passed a law in November banning all but police-sanctioned protests.