The forward admits his side struggled to gear itself up for Saturday's clash with Eintracht Braunschweig, while Arjen Robben claimed it was poor in the second half.
A brace from Arjen Robben sealed the Bavarians' 39th unbeaten Bundesliga game in a row, though the likes of Simeon Jackson and Karim Bellarabi nearly pegged the German champions back in the latter stages of the game.
And while claiming that die Roten's heavy schedule was responsible for a loss of sharpness, Muller underlined that his team must get back to their best if they are to continue their push for an unprecedented second successive treble.
"We did what we had to do. It wasn't easy to motivate ourselves after playing against Dortmund and the difficult [Champions League] game in [CSKA] Moscow," the 24-year-old told reporters. "We wanted to score a quick goal so avoid any problems.
"The cup game against Augsburg will be tough, it's a knockout match, so motivation won't be a problem. We'll need to be on our game."
Goal hero Robben likewise admitted the side was far from its best during the second half, adding: "We showed we have to concentrate and go all out right from the off.
"We did that in the first half, we wanted to score an early goal and played really well. Any criticism of the second half is fair - we didn't play as well."
Pep Guardiola's men have nevertheless opened up a four point gap at the top of the Bundesliga over second-placed Bayer Leverkusen.