The Germany international was said to have been a target for Louis van Gaal at Manchester United but has committed his future to Pep Guardiola's vision for the next five years.
"I am very happy to have extended my contract at Bayern until 2019," Muller told the club's official website.
"There were some very good discussions with the club who made me realise that I am in the right place here.
"I have the feeling that I am an important part of the club's plans. Bayern Munich has been my club since 2000 and it will remain so in the coming years."
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