The Germany international goalkeeper signed from Schalke at the end of the 2010-11 season and has enjoyed three successful campaigns in Munich, with his trophy haul including two league titles and a UEFA Champions League winners' medal.
Neuer's deal had been due to expire in 2016, but the keeper has agreed new terms that will see him remain at the Allianz Arena for another three years beyond that.
Bayern's chief executive officer, Karl-Heinz Rummenigge, was delighted to announce the news.
"Our goalkeeper Manuel Neuer has today extended his contract until June 30, 2019," he told the club's official website.
"It's also a mark of his wonderful character, because he's said: 'I want Bayern Munich forever!'
"I'd like to thank Manuel Neuer very warmly for this."
The news acts as a positive ending to a miserable week for Pep Guardiola's men, who were dumped out of the UEFA Champions League in the semi-finals by Real Madrid on Tuesday as the Spanish giants put four goals past Neuer in a 4-0 win that sealed a 5-0 aggregate success.
