With a second-leg quarter-final tie with Manchester United in the Champions League on the horizon, the Spaniard opted to field an under-strength team for the trip to Augsburg, with them having already sealed the league title.
Defeat meant that the Bavarian giants failed to become the first ever team to go an entire league campaign unbeaten in Germany's top flight, but Guardiola claims that an eventual loss was inevitable.
He told Bayern's official website: "We lost because the opponents were a little bit better than us. We saw how good Augsburg are in the DFB-Pokal.
"We fought hard and tried different approaches. That's football, that's sport. You can't always win. A defeat was on the cards sooner or later.
"We accept that and we need to prepare as soon as possible for the game against Manchester United."
Guardiola's side host United at the Allianz Arena in Munich next week with a slender advantage in the tie after securing an away goal in the 1-1 draw at Old Trafford on Tuesday.