The Spaniard believes his squad will be stretched to the limit over the coming weeks, with a number of first team players out injured
The likes of Xherdan Shaqiri, Claudio Pizarro, Franck Ribery, Bastian Schweinsteiger and Philipp Lahm are all missing for the Bavarians with a variety of knocks.
With the European champions set to enter a gruelling period in the season, Guardiola feels the support of the home fans could be more valuable than ever.
"This is a difficult situation," he told reporters at a press conference.
"I don't know that the condition of the team is. I hope that our heads are in the right place. When our legs have not got much in them, we need the support of our fans.
"We have to survive the next two or three weeks. That's why we have a second team."
However, Guardiola did confirm that Mario Mandzukic and Diego Contento can return to the fold for Saturday's match against Eintracht Braunschweig.
Looking ahead to the clash with the newly-promoted side, the former Spain international called upon his players not to underestimate the northerners, due to their impressive results against the Bundesliga's top teams.
He added: "They will be 100 per cent focused. For us, it is difficult to maintain that level."
Finally, the 42-year-old drew a line under the recent mole scandal, in which Bayern's line-up and tactics were leaked to Bild prior to their clash with Borussia Dortmund.
"This is normal at a big club. It happens. I'm trying to convince my players that it's best if things remain amongst us. The issue is over now."