Guardiola admitted on the eve of the game to Augsburg that his priority was the second leg of their Champions League quarter-final against Manchester United on Wednesday, and clearly had no regrets about taking such a stance despite the 1-0 loss.
"If this had been important, then Philipp (Lahm), Franck (Ribery) and Arjen (Robben) would all have been here," Guardiola said.
"The Bundesliga is over - that's in Bayern's museum already and is staying there.
"We tried to win and fought hard, but you can't always win in football and we've got to accept that.
"Now we've got to prepare for our final against Manchester United as soon as possible."
Guardiola's rotation did not receive much approval from the rest of the Bundesliga, though, with Eintracht Frankfurt coach Armin Veh critical of the way the champions snubbed the league.
"You can always lose to Augsburg - that's fair enough. But if you look at the team they sent out, then you've got to say that they were architects of their own demise," Veh told Sky television.
Schalke director of sport Horst Heldt added that it's "not good style", joking that "maybe they had a lot of injuries".
Bayern midfielder Toni Kroos defended Guardiola's team selection, saying it was "only normal that you do it when you're already champions".
He added: "It just didn't work out. We want to win every game - even (Saturday's). It doesn't mean we just gift games."