The result left the North African neighbours level on points and goal difference at the top of Group C, so they will meet again next Wednesday in Sudan to decide which country goes to South Africa.
Egyptian hostility
The build-up to the match had been marred by hostility between supporters, including stones being thrown at the Algerian team bus as it drove from Cairo airport to their hotel and Internet and media wars of words.
World football governing body FIFA confirmed to AFP news agency that three Algerian players had sustained injuries, potentially ruling them out of the showdown.
"We saw that three players had been injured - Khaled Lemmouchia on the head, Rafik Halliche above the eye and Rafik Saifi on the arm," FIFA representative Walter Gagg said.
"These weren't superficial injuries," he stressed.
For the Algerians, Egyptian security officials and the media added insult to the injuries by saying that the Algerian team faked the attack.
The Egyptian press reported that an initial investigation showed the Algerians had smashed the windows of the bus with emergency hammers.
Sigh of relief
But authorities in Cairo breathed a collective sigh of relief after the 2-0 result in favour of the home team saw concerns about violence ease.
Amr El Kahky, Al Jazeera's correspondent in Cairo, said: "Everybody is happy that the match went smoothly. No one was hurt, no provocations, there were no incidents that marred the game.
"They [Egyptian authorities] heightened the alert [since the bus attack]. They were really up to the mission, the game went safely. This nightmare has passed away," he said.