"My conclusion here is that Morsi is just the president of the Brotherhood, that's all. We are back to square one," since Mubarak's fall, said Sayed al-Hawari, who carried a plank of wood as a shield against the volleys of stones.
A liberal protester, Rania Mohsen, said, "We are here against turning the state to a Brotherhood state .... We do not want to replace the old regime with a new like the old one."
A Morsi supporter, in turn, accused the other camp of being "thugs" who chanted against the leader of the Brotherhood and harassed the Islamists during noon prayers in Tahrir.
"We have to give Morsi a chance," 19-year-old Moez Naggar, said. "The more protests we have, the less we can expect from him."
A schoolteacher who said he belongs to the Brotherhood expressed dismay over the violence, saying he was surprised by the other camp's anger at Morsi. Sherif Mahmoud pointed to Morsi's attempt to remove the prosecutor-general, who many across the ideological spectrum have said should be sacked.
"The prosecutor general is a corrupt man," Mahmoud said. "The president is moving step by step."
Around nightfall, fighting stopped as the Brotherhood supporters left the square in buses.
Rashad Bayoumi, deputy leader of the Muslim Brotherhood, told The Associated Press that the scene around Tahrir Square "is something everyone is ashamed of."
He said Brotherhood members did not take part in the clashes and that the group was there simply to demand judicial independence. Still, the clashes stopped at the time when the Brotherhood's party ordered its members to leave the square at 6 p.m.
Morsi was in Egypt's second largest city, Alexandria, for Friday prayers where he pledged that former regime figures would be brought to justice despite Wednesday's verdicts.
The 24 were acquitted of organizing the so-called "Camel Battle," an incident on Feb. 2, 2011, when a crowd of Mubarak supporters —including assailants on horses and camels — attacked protesters holding a sit-in in Tahrir to demand his ouster. Two days of fighting ensued, leaving nearly a dozen dead.
"All segments of Egypt's society were deprived of many rights" under Mubarak, Morsi told a crowd of supporters. "And the biggest right deprived of us was the right to freedom."
Following the acquittals, Morsi on Thursday moved to dismiss the country's Mubarak-appointed prosecutor general by moving him to the position of ambassador to the Vatican. However, the prosecutor, Abdel-Maguid Mahmoud, refused to step down and vowed to remain in his post, as law gives immunity to the prosecutor general from being ousted by the president.
Morsi's move also angered judges, who held overnight an emergency meeting denouncing the attempt to remove Mahmoud.
Many blame the prosecutor for frequent acquittals of police and Mubarak-era officials over the past year, saying he put together shoddy cases. Egyptians were also disappointed in what they saw as a weak verdict in the trial against Mubarak. He is serving a life sentence for failing to stop the killing of protesters last year, but prosecutors did not prove he ordered killings and he was cleared of corruption charges.