Algerians are celebrating the win, but Egyptians are concerned
The Egyptian government has recalled its ambassador to Algeria following complaints about violence towards football fans, reports say.
The move comes hours after Algeria's ambassador in Cairo was summoned to the Egyptian foreign ministry.
Sudan has also summoned the Egyptian envoy in Khartoum, angry at Egyptian media coverage of the game's aftermath.
The Algerian football team beat Egypt in a decisive World Cup qualifying match in Sudan on Wednesday.
They won the last African spot for the finals in South Africa next year.
And world football governing body Fifa has opened disciplinary proceedings against Egypt over the accusations the Algerian team bus was pelted with stones in Cairo.
The Egyptian government alleges 21 of its citizens were attacked after the match.
1978: Egyptian team recalled part-way through All Africa Games in Algeria after brawl following win over Libya. Algerian spectators joined in on Libyan side
1989: Egypt beat Algeria to reach Italia 90. After the match, midfielder Lakhdar Belloumi blinded the Egyptian team doctor with a bottle
1990: Egypt refused to send its team to African Nations Cup in Algeria
2009: Striker Hossam Hassan and brother Ibrahim Hassan banned indefinitely by Fifa after a brawl following a club game in Algeria
Egypt has recalled their ambassador for "consultations", the official state-run Middle East News Agency said.
The Sudanese foreign ministry announced it has summoned the Egyptian ambassador in Khartoum to hear complaints about the way Egyptian media covered the violence.
They say Egyptian comments about attacks after the game exaggerated the scale of the fracas, and insinuated the 15,000 Sudanese police deployed to the ground weren't in control.
"There were minor incidents, four people were lightly wounded," said Abdel Majid al-Tayeb, Khartoum police spokesman.
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.
Before the match in Cairo, three Algerian players were injured by rocks thrown at their bus as they arrived.
Violence between Egypt and Algeria fans flared up across four countries.
Following violence against Algerians in Cairo earlier this month, Egyptian businesses in Algiers were ransacked.
The rivalry between Egypt and Algeria is long and bitter
The Egyptian government called in the Algerian ambassador following reports of violence by Algerian supporters against Egyptian fans who travelled to the play-off in the Sudanese city of Khartoum, according to local media.
An Egyptian foreign ministry spokesman said the Algerian government also had a responsibility for the safety of Egyptians living in Algeria.
After the Cairo qualifier, which Egypt won 2-0 bringing the group to a deadlock, there were riots between supporters in the city.
A total of 32 fans were injured and the head of the Algerian Football Federation blamed his Egyptian counterpart for whipping up the tension.
In Algiers, Egyptian businesses were ransacked.
Even in France, problems were reported between the country's Egyptian and Algerian communities. Six boats were torched in Marseilles by Algerian fans and 500 police were deployed to quell clashes in the city.
Before the match in Sudan, Egyptian press commentators had called for Egypt to "reconsider" diplomatic relations with Algeria.