The Germans won 1-0 thanks to Mario Mandzukic's second-half goal to make it four wins from four in Group D.
Manchester City are just three points behind and can still pip them to top spot, though, with the two sides due to meet in Munich on the final matchday.
Guardiola told the Bayern website: "We want to finish first, so we'll have to beat (CSKA) Moscow (away from home in two weeks) and Man City."
Bayern's win was rather less convincing than the 5-0 thumping of the same opponents at the Allianz Arena last month but was their ninth in a row in the Champions League, equalling Barcelona's record from the 2002/03 season.
"Normally you might say that wasn't a match worthy of an entry in the Champions League history books - but in fact it was," chairman Karl-Heinz Rummenigge said.
Guardiola added: "I'm very, very happy we've equalled this record, and I hope we can extend it in Moscow. I'm grateful to (former coach) Jupp (Heynckes). He's made a bigger contribution to the record than I have."
The Spaniard admitted a repeat of the 5-0 result was never going to be likely in the Czech Republic.
He said: "We knew it wouldn't be possible for the game to go as well as it did in Munich. All matches in the Champions League are dangerous.
"Plzen are a very, very good team. And if you lose 5-0 like Plzen did, you're even more focused in the next match because you're determined to do better. We spoke about all this beforehand. We played very well in the second half and created plenty of chances."
Forward Thomas Muller felt the performance left a lot to be desired.
"We've not covered ourselves in glory, but we've won it, and that's the most important thing," the Germany international said. "We're not about to crack open the champagne.
"We simply made too many errors, and gave away possession far too easily in the build-up. Nor did we make the most of our chances. Plzen here at home are a completely different proposition compared to when they came to Munich."