"We have a few things to improve and one of them is that we gave Roma too many chances at the start of the second half," he told Sky Sport Italia.
Guardiola recognised that the game was atypical after Bayern scored five goals in the first 35 minutes on their way to their European record away win which left them top of Group E with maximum points.
"This game is an exception, an incident," he said. "It's not the difference between the two teams, we will see that in two weeks.
"We got a quick goal and that relaxed us, then we got another. Rome are a team who always play well, but we were very aggressive, made the right decisions and found space."
His opposite number Rudi Garcia took responsibility for the disaster.
"It was a technical collapse, not a mental one," said the Frenchman, whose last match against Bayern ended in a 6-1 defeat when he was coach of French club Lille two seasons ago.
"The first person to make a mistake was myself. I got the strategy wrong. In the second half, we showed some pride and would have scored more goals if it hadn't been for their goalkeeper."
"Bayern have showed that they are stronger than us. We were spectators at the match, we should have been more aggressive and compact," he added.
"We need to accept this defeat which shows how far we have to go to get close to the world's best teams. We can still qualify from this group, but not playing like this."
Midfielder Daniele De Rossi said the difference between the sides was not as big as the scoreline suggested.
"It's a stab in the heart, the city and ourselves had waited so much for this game," he said. "There was a technical imbalance, they are stronger than us. But I don't think the difference is as big as the scoreline suggests.
"This defeat can be a lesson for the future and shows us that there is a long road ahead. We got a bit demoralised because all they did worked and nothing came off for us."
Goalkeeper Morgan De Sanctis added: "The only positive thing about this evening has been the behaviour of our fans. This was an unjustifiable defeat. We all take the responsibility." (Writing by Brian Homewood in Berne; editing by martyn herman)
