Saul Niguez scored a stunning solo goal after 11 minutes to settle the match, with David Alaba's long-range shot against the crossbar the closest Bayern came to levelling matters for next week's second leg at the Allianz Arena.
Guardiola, who will leave the Bundesliga champions to coach Manchester City next season and feels his Bayern tenure may be defined by this Champions League campaign, made the bold call to leave star man Thomas Muller among the substitutes alongside Franck Ribery.
But he felt his team were well briefed to deal with the tenacious threat of Atletico, which overwhelmed them for large parts of the first half.
"Saul's goal is a great goal, he's a fantastic player. It is a result of our mistakes," he told beIN Sports.
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"It was a good game overall, but we started badly. The goal was a consequence of our slow play."
He added: "We have talked about Atletico's very strong starts to games before.
"That's not a great result for us. It's always unpleasant when you fail to score in the away game. But we still have 90 minutes to go."
The former Barcelona boss was satisfied with the overall quality of Bayern's play, but rued the slack defending that allowed Saul to net in thrilling style.
"We played really well and had enough chances to score," he said. "I'm satisfied with our performance.
"In the second leg we have to play very intelligent, we need patience. And we only need one goal to reach the extra time at least."