The Bundesliga champions defeated CSKA Moscow 3-0 at the Allianz Arena on Wednesday to finish the group stage with five wins from six matches, seven points clear of second-placed Manchester City.
Bayern came into the game already assured of their place in the last 16 as pool winners, but any notion of possible complacency was quickly quashed when Thomas Muller struck the opener from the penalty spot in the 18th minute.
Bastian Schweinsteiger, making his first start since the World Cup final, teed up Sebastian Rode for Bayern's second and the home side wrapped up a convincing win thanks to Mario Gotze's last-minute strike.
Having qualified for the knockout stages with ease, Guardiola was quick to hail the achievements of his players.
"I am proud of the entire squad," he said. "We were outstanding.
"We were better than the opposition in every game."
Rode's header six minutes from time was his first in the competition and the 24-year-old was delighted with the victory while thoughts were already towards Monday's draw.
"The first goal in the Champions League is always something special, but it's more important that we won this match," he said.
"Moscow played very defensively and we wasted some good chances. It was a nearly perfect group stage; it’s a pity that we lost at Manchester City.
"Now we are looking forward to the draw of the last 16 on Monday."
