Boateng’s contract with the Bundesliga champions expires at the end of the season and a mutual agreement has been reached to part company after a ten-year union.
The 32-year-old joined the Bavarians from Manchester City in the summer of 2011 and he has enjoyed enormous success at the Allianz Arena.
Boateng has so far won eight Bundesliga titles, two UEFA Champions League trophies, five DFB-Pokals, two FIFA Club World Cups, two UEFA Super Cups and two DFB-Super Cups with Bayern Munich.
With Bayern currently enjoying a seven-point lead over RB Leipzig in the race for the Bundesliga title, Boateng could depart with yet another league title.
"Jerome's contract expires in the summer and will not be extended," Bayern sporting director Hasan Salihamidzic told Sky Sport Germany ahead of Wednesday's Champions League quarter-final first leg with Paris Saint-Germain.
"He leaves through a big door, hopefully with more titles."
Boateng’s is the latest high profile player set to leave Bayern Munich at the end of this season, with David Alaba also departing at the end of the campaign.
A deal has already been struck for Leipzig defender Dayot Upamecano to augment for their loss.
Boateng was a member of Germany’s 2014 World Cup winning squad, amassing 76 caps in total.