Kasia Lenhardt, 25, was found dead in her Berlin apartment on Tuesday. Her death is not being treated as suspicious by authorities.
She and Boateng had separated last week, the latter confirming in a since-deleted social media post.
Bayern coach Hansi Flick confirmed Boateng had asked to leave the squad for personal reasons on the eve of their Club World Cup final against Mexican side Tigres, and he will be absent indefinitely.
Flick told a news conference: "This has stunned us.
"Jerome came to me and asked me to return home. After a negative [COVID-19] test, he will return home and not be available until further notice."
Boateng had played the 2-0 semi-final win over Egypt's Al Ahly on Monday and would have likely started again when Bayern go up against Tigres.
His experience and physical prowess will have been key in potentially nullifying the threat of in-form Tigres striker Andre-Pierre Gignac, who has netted in each of his previous six matches across all competitions.
Flick would not give any hints as to his selections, but has urged Bayern to take the initiative.
"It is up to us to put pressure on our opponents and to play our game when we have possession," Flick continued. "We did it well in the semi-final. I have full trust in my team.
"We have to be alert. Tigres are very quick in their build-up. They work well down the wings and have players in the centre who score.
"We have to be there from the start and convert our chances this time."
Flick's Tigres counterpart, Ricardo Ferretti, was in a bullish mood ahead of the match, adamant people are underestimating them ahead of this contest just because they are not from Europe.
He said: "You mention Bayern of Europe and nobody denies their achievements, but why do people only want to see things from one side?
"In 10 years we have won 11 titles. If you want to predict it [the game] because they are European and we are North American, it would be underestimating us.
"We know the capacity of Bayern, but as I have always said, we are not afraid of anyone. We will try to do our thing, very well, in order to be champions."