The Egyptians were also found guilty of overcrowding at the Cairo International Stadium and of detaining the Algerian bus for 45 minutes afterwards in the latest twist to a long-running soccer feud between the two nations.
FIFA's disciplinary committee fined the Egyptian Football Association (EFA) 100,000 Swiss francs ($88,160) for the incidents before the match on November 14.
Egypt won the game 2-0, leaving the teams level on points, goal difference and goals scored at the top of African Group C, but Algeria won a play-off five days later in Khartoum to qualify for their first World Cup since 1986.
"The FIFA disciplinary committee took this decision after determining that the EFA had failed to take all the necessary security precautions to ensure the safety of the Algerian delegation, as well as security and order at the Cairo International Stadium," said FIFA in a statement.
"The Egyptian FA had not adopted the necessary measures to prevent the assault on the bus of the Algerian delegation on the way from the airport to the hotel on Nov 12. In addition, the bus windows were smashed and four members of the Algerian delegation, including three players, were injured.
"It was equally noted that security and order in the stadium were not guaranteed, as 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."
At the time of the incidents, Algerian Minister of National Solidarity Djamal Ould Abbes called the Cairo violence "unacceptable and uncivilised" while Egypt recalled its ambassador from Algiers for consultations.
Bad feeling between the two sides stretches back to a World Cup qualifier 21 years ago in Cairo, when Egypt won 1-0 to guarantee a place at the Italy finals in 1990.
Players clashed on the field after that game and the Egyptian team doctor was partially blinded during the trouble.
Egypt then threatened to pull out of the following year's African Nations Cup in Algeria. They eventually sent a B team and lost all three group games.
