The 34-year-old Belgian international, who has not played for three months due to a broken foot and has scored four goals this season, joined the German team in 2006.
"We are delighted Daniel will continue playing for Bayern next season," said sports director Christian Nerlinger.
"We know exactly what we have with him. With his experience and qualities he will continue being an important part of our squad."
Bayern meet Chelsea in next month's Champions League final on home soil in Munich.
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