Guardiola was able to name just four substitutes as a result of Bayern's injury crisis but the Bundesliga leaders swept aside the visitors thanks to Robert Lewandowski's brace and a late Thomas Muller effort.
The win serves as ideal preparation for Wednesday's UEFA Champions League quarter-final with Porto, and Guardiola told Bayern's official website: "I'm very, very proud.
"Three days after the [DFB-Pokal] match in Leverkusen we play against the third-best attacking line-up in the Bundesliga. We dominated the game and played well, which pleased me.
"Now we need to recover and focus on a very special competition. I hope that we can compete with these players in Porto and that no more players will be hurt."
Lewandowski now has six goals in as many appearances for the Bundesliga champions of late, helping fill the attacking void left by recent injuries to Franck Ribery and Arjen Robben.
"We knew this was not going to be an easy game, especially after a cup game of 120 minutes, and just two days free, it is always difficult," the Poland international added.
"Nevertheless, we played very well, except for maybe the first minutes of the second half. But after the second goal everything was clear and we could loosen up.
"We could have scored more, but we are happy. "
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