The three were part of the 24-man squad named by coach Laurent Blanc last week but fresh injuries while on club duty mean France will be stretched as they try to wrap up qualification for June's finals in Ukraine and Poland.
"MRI scans... have shown that all three are unable to play in the matches," a federation statement said.
France lead Group D by a point from Bosnia with just the two qualifiers at the Stade de France left.
Regulars Philippe Mexes, Yoann Gourcuff, Abou Diaby and Guillaume Hoarau were already out with long-standing injuries and on Sunday Bacary Sagna pulled out after breaking his leg playing for Arsenal, leading to a call-up for Mathieu Debuchy.
Real Madrid striker Benzema is suffering from an abductor muscle problem, Bayern Munich winger Ribery has calf injuries and Paris St Germain midfielder Matuidi is struggling with thigh trouble.
Defenders Eric Abidal and Laurent Koscielny remain in the squad but are doubtful with knocks.
"It is part of the job of national coach," Blanc earlier told reporters about his squad's fitness.
"Players are subjected to quite a tough regime with [club] matches every three or four days and muscle injuries can multiply. Eric is very important to us. I really hope he will be fit to play."
A decision on possible replacements for the injured trio has not yet been made and depends on whether Blanc sticks to his usual plan of having one man up front or switches to 4-4-2 given that Albania are likely to play defensively on Friday.
France may try to attack more than normal as they need to beat Albania to guarantee they stay in front of Bosnia ahead of the final showdown with the Balkan side on October 11.
