"It was like a horror movie," said Mohammed Yehia, an activist and university student from the Nile Delta, who was among the protesters.
The confrontation marks a dangerous juncture in Egypt's three months of upheaval.
When longtime president Hosni Mubarak was ousted Feb. 11 after 18 days of mass demonstrations against his authoritarian rule, protesters hugged and kissed soldiers on tanks in Tahrir Square, praising them for protecting their "revolution." Most welcomed the handover of power to the Armed Forces Supreme Council, a body of top generals headed by Defense Minister Field Marshal Hussein Tantawi.
In the weeks since, tensions have risen. Protest leaders have been critical of the military council's handling of the post-Mubarak transition, and the public has been angered by its failure to prosecute the ex- president. But both sides also worked to stay on good terms.
The overnight clashes resembled the ugliest moments of the 18-day protest movement against Mubarak - with authorities cracking down violently and protesters chanting for the leader's removal. The violence only fed accusations among some protesters that the military - especially Tantawi, a longtime Mubarak loyalist - was only trying to preserve the ousted president's regime.
In the raid, soldiers detained 42 youth protesters, including a British and a German national, said human-rights lawyer Mohammed al-Ansari, and the protesters now face military tribunals for violating military bans on gatherings. The military said eight others with military uniforms were arrested, in reference to the dissenting army officers who joined the Friday protest.
The protest movement appeared deeply divided over how to react. Some demanded protesters push ahead with the confrontation with the military, while others warned a conflict with the army - Egypt's most powerful institution - would be disastrous for the movement, saying some form of coexistence must be found.
Democracy advocate Mohammed ElBaradei, whose supporters were among those who organized the wave of anti-Mubarak protests, said in a Twitter message that "dialogue is the only alternative." He said, "Confidence between the people and army" must be preserved "for the sake of the nation."
Egypt's largest Islamic group, the Muslim Brotherhood, also warned against any attempt to cause divisions between the people and the army, calling them "one hand."