The German giants were beaten 1-0 in the Champions League semi-final first leg at the Vicente Calderon courtesy of a superb individual goal from Saul Niguez in the 11th minute.
Bayern were by far the better of the two teams in the second half but Guardiola was left to lament why his players could not get past a sturdy Atleti defence which was bolstered by goalkeeper Jan Oblak.
"We need to think about who we were playing, the team that Atletico Madrid are," Guardiola said.
"They have a very good goalkeeper, they defended very well, with many people inside, it is not easy. Teams make very few chances against Atletico, we did create some, that is an argument we can make, not an excuse.
"We did not start well, but we played enough to score."
The return bout takes place at the Allianz Arena next Tuesday.