The match was the last of Bayern's three January friendlies and first-half goals from Sadio Mane, Jonathan Soriano and Robert Zulj saw Salzburg to the surprise win on Saturday.
Kevin Kampl also missed a second-half penalty for the hosts at the Red Bull Arena.
Guardiola said it was important he used the friendly to try new things ahead of Bayern resuming their Bundesliga campaign against Borussia Monchengladbach on Friday.
"I made some tactical changes today because we wanted to have one more player in the midfield," he said.
"Yesterday, we trained a new system with three defenders. This was mainly so that we could have the ball a little bit more in the midfield.
"We have to use these friendlies to try out new things, for me that is what they are about. Javi (Martinez) played 35 minutes with a little injury, so we had some problems.
"But again, friendlies are exactly for that. I can't test new things during the season. Pierre-Emile Hojbjerg can play as a central defender or in the midfield.
"However when you are three goals behind after the first half the coach goes crazy and the players sadly have to try to deal with that."
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