Marcus Alonso scored just before half time while Michy Batshuayi found the back of the net seven minutes from time to save some face for the Premier League champions.
Chelsea went behind early on as Rafinha put the German champions 1-0 up with a low shot from the right which took two bounces and skipped inside the far post and past Thibaut Courtois.
However, he did not move to Stamford Bridge to swap one seat on the bench for another and he did enough to suggest in his cameo in Singapore that he will prove a mobile and effective outlet for Chelsea this season.
"I chose to play in the Premier League and I want to play in Antonio's team", Morata told Chelsea'swebsite.
Chelsea tried to push for an equaliser but Bayern were able to hold form as they overcame the disappointment of slipping up against both Arsenal and AC Milan by registering an impressive win over the English champions.
"We have to learn from the experience when we won the league three years ago and then had a bad season, so we know that's what we have to work at", the defender said.
"I think the only way to know (if we can handle the increased workload) is to work, to work with my players", said the Italian.
"When you are the main striker for Chelsea you need to fight for all the competitions and if you are going to fight for all competitions you need your strikers to score lots of goals".
But German global Mueller, whose future has been rumoured to be in doubt after Bayern's loan signing of James Rodriguez, was the outstanding player in a competitive pre-season friendly.
Conte noted that preparing for the upcoming season while on tour overseas has become more of the norm for big football clubs.
He added: "After being champions two years ago, we had a bad season".
Chelsea's new record signing Alvaro Morata then made his Chelsea debut, replacing Jeremie Boga after 62 minutes.
"I hope to see the same tomorrow here (against Bayern)".
"I speak about Morata..."
He added: 'We didn't start as well in the first half.