The ex-Barcelona boss was unable to continue his excellent record at Santiago Bernabeu but insists he was proud of his players despite their defeat
The Spaniard had never lost as a coach at Madrid's stadium until Wednesday, when Karim Benzema's strike was enough to put the reigning European champions to the sword in the opening leg of their semi-final clash.
Guardiola insists he was proud of the way his players approached the game but acknowledged their lack of cutting edge ultimately cost them against Carlo Ancelotti's side.
"We lost," Guardiola said to Sky after the match. "It was a difficult game, but there is still a second leg and we will try to get every player in shape for that.
"Madrid have always played like this. They are so quick. They let you play and wait for you to lose the ball. You have to be very neat and very organised, and we did that. I am very, very proud of my team.
"There is no better team than Madrid and we just lacked a goal. Now we have to score two or three and we will work towards that."
There was a late shout for a penalty in Bayern's favour from Thomas Muller when the German forward went down under a challenge from Xabi Alonso as he tried to turn inside the area in the dying minutes.
However, the former Barcelona boss responded "no, I don't think so," when asked if a spot kick should have been given.
The Bavarians will aim to turn the tie on its head when they host Madrid in the return leg next Tuesday.