Thomas Muller scored a first-half penalty to settle matters, making it two wins from two for the Bundesliga champions in Group E, but it was the eerily quiet Arena Khimki that caught the visiting coach's attention.
CSKA were forced to play the match behind closed doors after being sanctioned by UEFA for the behaviour of their fans, who displayed "a range of racist and far-right symbols" in a Champions League match with Viktoria Plzen last December.
That left Guardiola disappointed, with Bayern's usually vast and vocal following consigned to watching on television.
"Football is about the supporters," Guardiola said.
"I hope we don't have to play behind closed doors again."
Those sentiments were echoed by chief executive Karl-Heinz Rummenigge, who added: "It was a strange game. There was no atmosphere or emotions."
Match-winner Muller, who also scored from the spot when the sides met in last season's Champions League, sent his penalty straight down the middle and revealed his confidence as he stepped up.
"I have a special technique for taking penalties," the World Cup winner said. "But, as long as it goes in, it doesn't really matter."
