Riot police in the Egyptian capital, Cairo, pushed back a violent demonstration near the Algerian embassy in the early hours of Friday.
Egyptian protesters reportedly hurled firebombs at police protecting the embassy and overturned a police van.
Egypt's Interior Ministry said 35 people were injured.
The clashes stem from Egypt's defeat by Algeria in a World Cup qualifying match on Wednesday, securing Algeria the last African place for next year's finals.
On Friday Alaa Mubarak, the son of Egypt's president Hosni Mubarak, made a rare public statement calling for a "tough stance" to be taken against Algeria.
"When you insult my dignity... I will beat you on the head," the businessman, who had attended the game in Khartoum, said.
On Thursday night around 1,000 Egyptians burned Algerian flags in a street near the Algerian embassy.
The protests continued into the morning, with 15 cars reported damaged, along with a number of shops. The ministry said 11 police officers were among the injured.
On Friday afternoon, worshippers leaving a mosque in the neighbouring Mohandisseen district gathered after prayers to again burn Algerian flags and chant anti-Algerian songs.
Algeria beat Egypt 1-0 in a play-off in Sudan, to clinch the last African spot for the finals in South Africa next year.
Protesters were incensed by reports that Egyptian fans at the match had been attacked as they left the stadium.
"We should treat Algeria like any country that has declared war on us," university student Amr Higazi told Agence France Presse.
The BBC's Christian Fraser in Cairo says demonstrations like this are normally broken up well before they begin.
Meanwhile, Egypt has threatened to quit international football for two years after complaining to Fifa over Algerian fans' behaviour in Khartoum.
The statement by Egypt's Football Federation added: "Egyptian fans, officials and players put their lives at risk before and after the game, under threat from weapons, knives, swords and flares".
Diplomatic spat
Egypt's foreign ministry had summoned the Algerian Ambassador to hear complaints about reports of attacks on Egyptian fans in Khartoum and on Egyptian businesses in Algeria.
The Egyptian ambassador in Algiers was than recalled "for consultations".
Sudan has also summoned the Egyptian envoy in Khartoum, angry at Egyptian media coverage of the game's aftermath.
The Egyptian government alleges 21 of its citizens were attacked after the match, but Sudan says many fewer were injured.
The teams needed the play-off in a neutral country to decide on qualification after the final group match between them on Saturday saw Egypt win 2-0, meaning the two teams finished tied at the top of the group with equal points and identical goal difference.
World football governing body Fifa has opened disciplinary proceedings against Egypt after the Algerian team bus was pelted with stones in Cairo before the match.
Three Algerian players were injured by rocks thrown as they arrived.
Violence between Egypt and Algeria fans flared up across four countries.
Source: BBC
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