The pair, who are both 20, have earned regular places in the Bayern team this season under coach Louis van Gaal and Müller has been called up to the full Germany squad having also played for the national Under-21 side. Their contracts were due to expire in June 2011, but the pair have been rewarded with three-year extensions after proving themselves in both the Bundesliga and Champions League this season.
"Both have progressed in a satisfactory way," said Bayern chairman Karl-Heinz Rummenigge.
"They graduated from our academy and they are the type of player we want to have, like (Philipp) Lahm or (Bastian) Schweinsteiger."
Müller has benefited from injury to both Bayern's stars Franck Ribery and Arjen Robben, while his performances have kept Germany striker Miroslav Klose on the bench. Having been called into the extended Germany squad for fitness testing recently, Müller has a chance of playing in this summer's World Cup in South Africa which will be held from June 11 to July 11. Likewise, Badstuber has made 20 Bundesliga appearances and cemented his place in Bayern's defence with a string of impressive performances.