The Real Madrid midfielder tore cruciate ligaments in his right knee during Germany's friendly against Italy on Friday and is expected to be out for at least six months.
Khedira had an operation on Saturday, but Matthaus believes he will face a race against time to make the finals in 2014.
"I feel very sorry for him (Khedira)," the 52-year-old told the Bundesliga website. "It's a really serious injury, as I know from personal experience.
"Hopefully he can still make it, but it's going to be tight.
"He'll need five to six months to get back in action and after that you've still got to find your old form. It's a race against time and it's a real pity for him, so soon before the World Cup."
The World Cup-winning captain believes Germany are in a strong position if Khedira fails to return to fitness in time.
"(Joachim) Low is in the fortunate position of having top-drawer alternatives in every position," Matthaus added. "Ilkay Gundogan and Bastian Schweinsteiger are on the way back themselves and the Bender (Lars and Sven) twins are ready to step into the breach as well.
"Philipp Lahm's another option as well now in a holding midfield role.
"Jogi Low's always come up with something over the past few years and he'll be able to compensate for the absence of Khedira as well."
