The German and European champions went into the game at the Doosan Arena expected to win comfortably, having thrashed the Czech side 5-0 on home soil in their previous meeting.
But laboured attacking play and a fine display from home goalkeeper Matus Kozacik kept Bayern out until Mario Mandzukic struck just six minutes after coming off the bench.
Bayern have won each of their four Group D games so far, and Kroos was keen to focus on the game's positives, despite a tough outing.
"We didn't have a great start but created more chances as the match progressed," he said.
"We had some good spells with a lot of possession in midfield but we also gave the ball away too easily when we approached their box.
"It is not easy to qualify for the knockout round after just four matches. We can be proud of this, but we still have some room for improvement."
The win was Bayern's ninth Champions League triumph in a row, matching Barcelona's record set in the 2002-03 campaign.
Goalkeeper Manuel Neuer, who was rarely tested throughout the clash, echoed coach Pep Guardiola's words before the match that the Bavarians are lacking a cutting edge against teams they are expected to dominate.
"We didn't start well," he lamented. "In the first 10 minutes Plzen had two corners and we could not get our rhythm going.
"Against teams like this it is important to use the full width of the pitch and circulate the ball well.
"Matching Barcelona's record is great for us but we were really hoping for a better performance."
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