The assailants hurled stones at the protesters and attacked with clubs.
Officials from deposed President Mohamed Morsi's Freedom and Justice Party said they heard gunshots in the square as well.
The clashes come two days after seven people were killed and more than 200 wounded in fighting between Morsi loyalists and security forces in and around Cairo.
Supporters of deposed Egyptian President Mohamed Morsi called on Wednesday for more mass demonstrations, declaring a “day of steadfastness” to protest against the formation of a new interim cabinet, which began its first day on the job.
Muslim Brotherhood supporters also accused the Egyptian military of having staged a coup against the country’s first democratically-elected leader.
Moreover, more than 500 academics in Egypt announced to have rejected the military coup in Egypt.
Some 556 academics from different universities in Egypt announced that they rejected the military coup which took place on July 3 and deposed legal President Morsi.
The academics after collecting signatures for a petition expressed objection to the coup.
Meanwhile, Egypt's interim government cancelled Morsi and former government officials' diplomatic passports, said sources from the Egyptian Ministry of Foreign Affairs.
NJF/NJF