Guardiola fielded a weakened side for the loss and came in for criticism from other Bundesliga coaches, but stressed that the European game took precedence.
"If this had been important, then Philipp (Lahm), Franck (Ribery) and Arjen (Robben) would all have been here," he 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."
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