Morata only signed for the Premier League champions on Friday but came off the bench in Singapore and set up Michy Batshuayi for Chelsea's second.
The Spain international was introduced just after the hour and was able to flick Cesc Fabregas' corner into the path of Batshuayi to score with five minutes to play.
And despite his lack of time with the Chelsea squad, Conte was happy with what he saw from his new signing and expects him to get even better.
"It's not easy to speak about the impact of Alvaro because he's only been with us two days and he needs to work and find his feet, and understand our idea of football, but for sure he showed a great will and for us he's a great buy," he told a media conference.
"We need to give him the right time to adapt to our way of football but he must be pleased with his performance."
It was a first defeat of pre-season for Chelsea after beating Arsenal 3-0 on Saturday, and although naturally disappointed, Conte found plenty to be happy with.
"We conceded three goals in half an hour and it's not simple, it was a difficult situation but the reaction was very good," he added.
"We didn't give up and the commitment was good. We tried to fight. Our start wasn't good but the players showed me a great will to try to change the result. We are only in pre-season and we are working very hard.
"Bayern are a top club, one of the best in the world. Regularly they win the league in Germany and in the Champions League they normally reach the final or semi-final, but we must take the positives and continue to work."