The coach says his side need to improve their first-half performance against Viktoria Plzen and praised Mario Gotze's efforts since recovering fitness
Bayern have two wins out of two in Group D, beating CSKA Moscow 3-0 in their opening game before turning Manchester City over at the Etihad Stadium in a 3-1 triumph.
The Bavarians can surge to nine points with a win over the Czech Republic side, though the Spaniard expects stiff opposition at the Allianz Arena.
"I have a lot of respect for our opponents," Guardiola, 42, told reporters on Tuesday. "I saw them against Manchester City and they performed very well in the first half.
"They have some excellent players and play nice football. The team have changed a bit since I was at Barcelona [who faced Plzen in 2011-12] but their philosophy remains the same.
"In the Bundesliga recently, we have been poor in the first half but I don't expect this to happen tomorrow."
Mario Gotze stole the limelight for the first time as a Bayern player in Saturday's 4-1 win over Mainz after coming off the bench to inspire a turnaround.
And Guardiola is pleased with his efforts since recovering fitness, while praising skipper Philipp Lahm's spell in midfield.
"I need all my players because everyone in the squad is important," the ex-Barcelona boss added. "Gotze is one of those players who thinks quickly on the pitch and I've been impressed with him since coming back from injury.
"Playing Lahm in midfield was an experiment and he did extremely well. I know he is a full-back and he will resume that position, but don't forget about Rafinha."