Khedira has "matured" into one of Germany's strongest midfielders in recent years and become just the kind of player Beckenbauer says Bayern have been lacking in a trophyless two seasons.
"Khedira is one of those prototypes - one who is prepared to sacrifice himself for the sake of the team," he told the Tz newspaper.
"You can hardly find those kinds nowadays, and you really need players like that in your team.
"I have not been pleased with the last two years for Bayern - if you only give 70 or 80% of your potential, then that is just not enough and that is the problem."
The most frequent accusation levelled at Bayern since they lost the final of the Champions League to Chelsea in May is that they did not have characters like Stefan Effenberg, Oliver Kahn or Jens Jeremies within their side who would intimidate their opponents.
Beckenbauer says such players are just as important as the most technically gifted individuals.
"But you don't just get players like them so easily," he added. "Khedira has matured into a real leader and players like him are a rare commodity nowadays.
"Today [Friday], players are almost exclusively wizards - everybody wants to play like Lionel Messi, but there is only one Messi."