The Belgian, who is set for a place in Bayern's starting XI in the Champions League final due to the suspension of Holger Badstuber, has been with the club since 2006, although he has only made 13 appearances this season, the last of which came in January.
Since then, he has been sidelined with a broken toe, but he is now on the road to recovery.
He has played a total of 133 games for the Bundesliga club and can now expect to add more to that tally next season.
"We are pleased that Daniel will still be playing for Bayern Munich next season," said Bayern's director of sport Christian Nerlinger on his club's website.
"We know what we get with him. His qualities and experience will remain an important component of our squad in future."
The former Manchester City defender has won the league and cup double twice during his six years with Bayern and is set to take part in his second Champions League final against Chelsea on May 19.