The treble-chasing Bavarians, five points clear of their rivals with nine matches left in the Bundesliga, play a second leg against Juventus in the round of 16 next week after a 2-2 draw in the first game.
But Bayern, seeking a record fourth consecutive German title, have managed just one point in their last two league games.
"Every game is a final for us now," Guardiola told reporters on Friday.
"There is not much space when you play Werder, it is complicated," he added.
News that makes sense
Your trusted source for staying up-to-date with the world around you. Get free daily news updates and analysis, straight to your inbox.
"They play a five-man defence and in front of that four midfielders. We will need patience, a lot of patience and we can't allow them any counter-attacks."
Guardiola welcomed the return to training on Friday of defender Javi Martinez, who underwent knee surgery last month, but said he would need more time before playing a match.
Top Werder striker Claudio Pizarro was ruled out by a muscle injury picked up in training, a major blow for his side. The 37-year-old former Bayern player has scored 11 times this season, nine since the winter break, including four goals in the last two league matches.
"He is one of the best centre forwards I have ever encountered. I hope he plays but as far away from our box as possible," Guardiola had said before the news of the Peruvian's injury.
(Reporting by Karolos Grohmann; editing by Andrew Roche)
