The Germany international, 25, has not played for the Bundesliga champions since suffering a cruciate ligament tear in his knee against Borussia Dortmund in December 2012.
A recurrence of the same injury last May forced Badstuber into another stint on the sidelines, but the defender was finally reunited with his team-mates on the training field on Thursday, though a first-team return may have to wait a little longer.
In a further boost for Pep Guardiola's side, winger Xherdan Shaqiri stepped up his recovery from a hamstring problem, and is hopeful he can be fit to feature in the DFB-Pokal final against Borussia Dortmund on May 17.
"I hope I'm ready for selection again in the cup final and can help the team there," the Swiss told Bayern's official website.
The Bavarians are looking for a swift response to their demoralising 5-0 aggregate Champions League exit to Real Madrid in midweek when they visit relegation-threatened Hamburg on Saturday.