The La Liga side claimed a 4-0 win in the second leg of the tie to progress to the final 5-0 on aggregate, knocking out the defending champions.
The Bayern manager told reporters: "If you don't play well and you defend set pieces badly, that's just how it is.
"We are playing at the highest level in Europe, and such mistakes are punished right away. Bayern are a big side. I will try to lift the players again."
Bayern face Hamburg in the Bundesliga on Saturday.