The 25-year-old was already under contract until 2015 but will now remain with the German champions until June 2018, the club confirmed on their website.
"I am very happy," said Boateng, who joined Bayern in 2011 from Manchester City. "Bayern are one of the biggest football clubs in the world.
"I enjoy every day working with the team."
He also thanked the club for taking a risk on him after an injury-hit spell in England.
"They bought me at a time when I was injured," he said. "I felt confidence, even when things were not going so well.
"I'm glad it worked out with the contract extension."
Bayern sporting director Matthias Sammer added: "The club are very pleased with Jerome. We know how much he has developed and the part he has played in our success."