The Bavarians have been without a number of first-team stars in recent weeks with Holger Badstuber, Javi Martinez and Thiago Alcantara all absent while Mario Gotze and Bastian Schweinsteiger have been struggling for fitness.
But Guardiola has fired a warning to other Bundesliga sides, insisting that his team can only improve on their early-season showings - if they correctly carry out his instructions.
"I am convinced that we will be even better when all the players are fit," he told the club's official magazine.
"But we will only be in the hunt for titles at the end of the season if each player accepts my decisions in this great squad.
"Otherwise, we have problems. I am a great friend of my players when they accept what I say. I support those who accept my decisions but those who do not want to understand will sit in the stands. I say again: we need all of our players."
Guardiola took over from Jupp Heynckes this season and admits that when he got the call to become Bayern coach, he made an instant decision to accept the role.
"From the first contact I had with Bayern, I knew within seconds: you have to do it," he said.
"I did not want to pass up the opportunity to work here with this great team that the club had put together in the past few years. Had I said no, I might not have been asked again."
Bayern sit top of the Bundesliga after eight games and have already demonstrated their class with fine domestic and European displays, most notably a 3-1 win against Manchester City at the Etihad Stadium.
And the Spaniard has been pleased with what he has seen from his side so far.
"It's not all that important to be top of the table in October, but it's always nice to be there," Guardiola continued.
"All that matters at the moment is that we get to grips with our playing style. It's an ongoing process and the performances against Manchester City and Leverkusen show we've already reached a decent level that we want to maintain in the coming weeks.
"I'm honestly really surprised how quickly the players have taken my ideas on board. We definitely need more time, but the level is already very, very high ... I'm happy how we're playing."