The club's CEO Karl-Heinz Rummenigge and the player were both delighted with the new deal, which will now see Boateng remain at the club until the summer of 2018.
"Jerome has developed a lot during his time at the club, and he is now one of the key players," Rummenigge told the club's official website. "For this reason it was natural that we would try to extend his deal. We have agreed this today and are all very happy."
I'm happy," Boateng said. "Bayern are one of the great clubs in world football to play here not only is enjoyable, but it is an honour. I want to achieve a lot with the club in the years to come."
Boateng joined the club in 2011 from Manchester City.