The Germany No.1's previous deal was set to expire at the end of the 2015-16 season, but the 28-year-old has now committed himself to the Bundesliga champions until June 2019.
Bayern CEO Karl-Heinz Rummenigge confirmed the news at an extraordinary general meeting for the club, in which Karl Hopfner was confirmed as Uli Hoeness' replacement as president, and paid tribute to the former Schalke goalkeeper's "wonderful character".
"Our goalkeeper Manuel Neuer has extended his contract until June 30, 2019," Rummenigge said at the event on Friday.
"The deal is amazing, great. It is also a sign of his wonderful character, that he said 'I want to be at Bayern forever.' I would like to express my gratitude to Manuel Neuer."
Neuer, who joined from Schalke in 2011 for a fee of €18 million, has made 48 appearances in all competitions for Bayern this season.