Guardiola rested several players for the match, ahead of Friday's UEFA Super Cup clash with Chelsea, and the Bavarians saw their 100 per cent record in the league end with the result, which came about when Nicolas Hoefler equaliser after Xherdan Shaqiri opened the scoring.
Guardiola, however, said he was proud of his players' performance during the match.
"I think it was a good game, for the audience, for the Bayern manager, and for the players," he said.
"And I congratulate Freiburg for their good performance. And I'm proud of my team, I think they've played very, very well.
"I know how difficult it is and how dangerous Freiburg were. Very soon we need to start preparing for the UEFA Super Cup final next Friday in Prague and I think we have made a good step forward today in our style of play."
Bastian Schweinsteiger was forced off late with an ankle injury, and Guardiola was unsure if he would be fit to play against Chelsea.
The Bayern boss said his team would be going all-out against the Blues, who famously upset his club in the 2011-12 Champions League final.
"We will prepare this final as well as possible," he said.
"We have to recover well. We only have three days, that's not much.
"The final is in our thoughts, we will play well, we will attack, we will try and control their counter attacks and the final will be good for the game for Bayern."
