The Bundesliga champions suffered a 1-0 defeat to Augsburg, with Guardiola resting the likes of Franck Ribery, Philipp Lahm and Arjen Robben ahead of the second leg of their Champions League quarter-final tie against Manchester United on Wednesday.
Guardiola has admitted that the Champions League is now his side's priority after wrapping up the league title and had no regrets about resting his key players despite the loss.
"If this had been important, then Philipp [Lahm], Franck [Ribery] and Arjen [Robben] would all have been here," Guardiola told reporters. "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."
Bayern are still 20 points clear of second-placed Borussia Dortmund in the league table.