The angry sitters-in attacked the shops with batons, rocks and birdshot pellets.
The attacks caused material damage to a number of shops.
Most of the shops shut their doors and turned off the lights after hit-and-run operations were reportedly undertaken by protesters and shops' owners.
A number of protesters have been holding a sit-in in the square since November 22, 2012 when President Mohammed Mursi issued a constitutional declaration,.
Clashes broke out between the protesters and their attackers, who removed the road blocks erected by the demonstrators.