During a 1-1 draw with Russia on Thursday, a laser was shone into the eyes of opposing goalkeeper Igor Akinfeev as Yacine Brahimi prepared to take a free-kick wide on the left for Algeria.
Moments later, Akinfeev came to palm away the cross but made no contact, and Islam Slimani headed into an empty net from six yards.
That equalising goal was enough to see Algeria through to the second round for the first time in their history, and Russia coach Fabio Capello lamented the use of the laser.
"He was blinded by the laser beam," he said.
"There are pictures. You can see that in the footage. This is not an excuse, it is a fact.
"There was a laser. I have never come up with excuses to get by in my entire life."
A statement released by FAF on Monday read: "The Disciplinary Committee of the Federation Internationale de Football Association (FIFA) has condemned the Algerian Football Federation to pay a fine of CHF 50,000 (Swiss francs) and also issued a reprimand against the FAF for inappropriate behaviour of Algerian fans at matches played by the national team at the World Cup.
"The Algerian Football Federation deplores the irresponsible behaviour of some fans and recalls that pyrotechnics and lasers are strictly prohibited in the football grounds.
"FAF launches an appeal to all fans who come to support their national team that they act with civility and have impeccable behaviour when expressing their support for their team.
"This will prevent a new sanction which, after received blame, could mean a suspension."
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