The Germany international, who had been out of action since December 2012, started Sunday's DFB-Pokal win at Preussen Munster.
The Germany international had been out of action since tearing his anterior cruciate ligament in a Bundesliga clash with Borussia Dortmund on December 1, 2012.
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However, Badstuber made his long-awaited comeback on Sunday, playing 79 minutes of Bayern's DFB-Pokal first-round clash with Preussen Munster.
"First game. Done!!!," the 25-year-old defender wrote on Twitter. "Thankful to be back on the field... It is simply the best!!!"
Badstuber's return is a timely one for Bayern, with Javi Martinez having been ruled out of action with a knee injury sustained in Wednesday's DFL-Supercup loss to Dortmund, and coach Pep Guardiola was in an upbeat frame of mind after his side saw off Preussen thanks to goals from Mario Gotze, Thomas Muller, David Alaba and Claudio Pizarro.
"Thank you to the people here," the Catalan stated. "And congratulations to my players for their professionalism."
Bayern begin the defense of its Bundesliga crown with a game against Wolfsburg at the Allianz Arena on Friday.