The visitors cruised to a convincing and deserved victory at the Camp Nou to hand Barca a disappointing start to their European campaign.
Koeman couldn’t fault his players’ attitude after the match but conceded there was a big difference in quality between the two teams.
“There were only three strikers available,” he said.
“Tactically there were moments in which we were in control. Bayern’s game is in the middle third and you have to fill [the gaps] there.It is what it is for the time being. I cannot complain about the attitude, but there is a difference in quality.
“They a team that as a group have been together for a long time and also have a bench that has improved.”
One of the few positives was the sight of Barca ending the match with a host of youngsters on the pitch, including Gavi, Alex Balde, Oscar Mingueza, Pedri and Yusuf Demir.
Koeman is hoping things will get better as the youngster mature and with a host of injured attackers set to return in the coming weeks.
“We have many young players who in two or three years will be better,” he said.
“It is very difficult to accept it, but we have to wait for things to improve and players to recover from their injuries.
“It is what it is, we have to spend a few weeks like this because later we are going to get players like Aguero, Dembele and Ansu Fati back.”
Barca’s next game in the group is a trip to Benfica on September 29. The Portuguese side drew their opening game 0-0 against Dynamo Kiev in Ukraine.