The boss will be concerned to have lost Riyad Mahrez, Aymeric Laporte and Phil Foden during the game through injury against the Bundesliga giants with the FA Community Shield against Chelsea less than a week away.
City fell two goals behind with only 23 minutes played at the Hard Rock Stadium, but in the balmy Miami heat, Bernardo Silva (2) and Lukas Nmecha ensure the Blues finished the US tour on a high.
Mahrez departed the pitch with an ankle injury on 28 minutes, Laporte left the field on 66 and Foden on 85 – the latter with what appeared to be a tweaked hamstring, though it is too soon to tell the extent of the three knocks at this stage.
On Mahrez, Pep said: “I don’t know how he is. I haven’t been in the locker room. He had a little bit of a problem with the ankle. I am concerned for many things - injured players and players who are not here.
"At the end, we played well and we tried to play. We have to convince the players that it is the best way. We have come here with a lot of young players and just one professional player from the first-team at the start - Claudio Bravo because Laporte was injured.
“On the other side, I am so satisfied for this tour and what these guys have done. It was the same in the previous two games - I said how proud I was”
The Blues’ boss was particularly pleased with how his young side coped with adversity and recovered to beat one of the best teams in Europe.
“The result doesn’t matter,” he said. “We analysed our mistakes and we did better. We have played together for a longer time now and we played against Bayern - one of the best teams with quality players.
“We were able to play good football and keep calm in the situation, even when we were 2-0 down.
“We started really well and created chances. When they arrived, they were so clinical. They have players like Robben and Wagner, and that was the difference. They have exceptional players.
“We kept going and we scored the goal through Bernardo at the end of the first half. Against Liverpool, we lost because the first goal was offside, and they had a ridiculous penalty.
“I said in the press conference that it didn’t matter. What does matter is the way we played and competed against Liverpool and it was the same today.
It was a huge experience for the future; for the players to think: ‘Okay, we can do it - we are able to play in our way against good teams,’
“We have five or six days to our first game and we don’t know which players are able to play but I am so satisfied. We will come back to Manchester in the best way.”
Though Leroy Sane didn't feature, the boss confirmed he wasn't injured, will work on his fitness and should be available against Chelsea next weekend.