FIFA ruled Tuesday that Egypt must stage its first two home matches in qualifying for the 2014 tournament at least 62 miles (100 kilometers) from the capital.
FIFA's disciplinary panel said Egypt's federation "failed to take all the necessary security precautions to ensure the safety of the Algerian delegation."
It also fined the Egyptian federation 100,000 Swiss francs ($88,000).
The meeting between the north African rivals last November was predicted to be volatile. Egypt had to win to keep its qualifying hopes alive and prevent Algeria reaching the tournament in South Africa.
On arriving in Cairo, Algeria's team bus was being driven from the airport when it came under attack from fans hurling rocks.
"The bus windows were smashed and four members of the Algerian delegation, including three players, were injured," FIFA said in a statement.
Security and order in Cairo International Stadium — which had a declared attendance of 75,000 — "were not guaranteed," FIFA said.
"An excessive number of spectators were granted access to the stadium, and the entrances and stairways were obstructed. Furthermore, at the end of the match, the bus of the Algerian delegation was detained for over 45 minutes."
Egypt 2-0, getting a goal in the fifth minute of stoppage time to force a playoff in neutral Sudan the following week. Algeria then won 1-0 to qualify.
The Desert Foxes will play England, the United States and Slovenia in Group C.