Japan ace Honda had a great chance to score early in the second half but took too much to survey his options before Bayern keeper Manuel Neuer stole the ball from his feet.
However, Honda gave the Russians some semblance of hope just after the hour-mark when he sent Neuer the wrong way from the spot after Dante was harshly judged for handball.
But as Bayern normally do, they tightened the screws and managed to win a penalty of their own with Thomas Muller converting after Robben had been brought down.
The loss left Honda's CSKA sitting second bottom in Group D on just three points while Bayern's win allowed them to set a new record of 10 consecutive victories in the Champions League.
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