Bayern suffered a 3-2 UEFA Champions League loss at the Etihad Stadium on Tuesday - their first in this season's competition.
The German champions were already assured of a place in the last 16 prior to succumbing to a Sergio Aguero hat-trick and Guardiola insists defeat has done little to harm the atmosphere among his players.
"The mood inside the camp is good even though we lost," he said. "I'm still proud of my team."
Guardiola's men - who are seven points clear at the top of the Bundesliga - visit Hertha Berlin on Saturday and the Spaniard knows the importance of picking up a positive result ahead of a busy schedule, made harder by Bayern's lengthy injury list.
"There's only three weeks before the winter break," he continued.
"We have a game every three days and we can't afford to rotate much.
"We're a good team, but not perfect."
Thankfully for Guardiola, he has no fresh injury concerns to deal with, and, when questioned over his recent tendency to change the team's system, he added: "The system isn't the most important thing, the idea is."
