Bayern return to league action on Saturday with a trip to their local rivals, as they aim to end a two-match winless run.
A 3-3 Bundesliga draw against Hoffenheim was followed by a 1-1 stalemate at Old Trafford in the first leg of their UEFA Champions League quarter-final on Tuesday.
Bayern have already won the Bundesliga title and with that in mind, Guardiola will rest some players ahead of the second leg against the Premier League champions.
"Augsburg is a very, very important game, but the match on Wednesday against Manchester is even more important," he said at a press conference on Friday.
"I'm going to rotate the team and the squad a little bit, we can try out a few things ahead of the United match.
"(But) it has to be a fair competition and we must show respect to our opponents, so we'll try and win the game."
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