Troops beat hundreds of protesters with clubs in Tahrir Square during a pre-dawn raid on Saturday.
One person was killed and dozens were injured.
Troops have since withdrawn, but the rallying continued. Many protesters are refusing to leave until the defense minister, Field Marshal Mohammed Hussein Tantawi, resigns. Tantawi, a Hosni Mubarak appointee, leads the Supreme Council of the Armed Forces, which rules Egypt now and is made up of the military's top generals.
Many Egyptians still feel mistrust toward the military that took over when Mubarak was forced out of office.
The overnight clashes resembled the ugliest moments of the 18-day protest movement against Mubarak - with authorities cracking down violence and protesters chanting for the leader's removal.
The Health Ministry issued a statement saying only one person was killed and 71 wounded, some of them with gunshot wounds, including three in critical condition.
The U.S. State Department called reports that excessive force was used in the square "disturbing" and urged the military to investigate. "People everywhere, including in Egypt, must have the universal rights of assembly and protest," it said in a statement.
The Associated Press contributed to this report.