Viktoria Plzen coach Pavel Vrba conceded his side have it all before them to surpass the UEFA Champions League group stages.
The 49-year-old saw his team give up an early lead in St Petersburg on Wednesday only to suffer defeat, leaving the Czech outfit without a point through two matches.
CSKA's home match was relocated from Moscow to St Petersburg after the Russian club's ground was rendered unplayable due to heavy rain.
Frantisek Rajtoral scored the opener for Plzen in the fourth minute but CSKA got back into the match thanks to two goals on the counter-attack from Zoran Tosic and Keisuke Honda.
A terrible own goal involving Plzen defender Radim Reznik and goalkeeper Matus Kozacik made it 3-1 for CSKA in the 78th minute and while Marek Bakos notched Plzen's second with a header in second-half stoppage time, Vrba was left to rue his team's missed opportunities in the first half.
"We started well and had two or three chances to score but we failed to take them," Vrba said.
"Then we conceded goals from situations which we had prepared for, because of mistakes with our passing.
"I must praise my players' efforts in the second half and for fighting until the end for a point but we made it hard for ourselves. The situation we are in now is very difficult."
Bayern Munich lead the group of six points from two victories, after they defeated Manchester City 3-1, while the English club and CSKA have three points apiece to sit clear of bottom-placed Plzen.
With four games to go in the group stage, Plzen will have to win at least two and pick up a point from another match to advance to the round-of-16.
While Vrba was disappointed his team wasted goal-scoring opportunities in Russia, he was thrilled with Plzen's response in the second half and thought they could have claimed a draw but for Reznik's own goal.
The right fullback's back pass with 12 minutes remaining looked easy for goalkeeper Kozacik to control but the Slovak gloveman let the ball slip under his foot and roll into the net, which effectively ended Plzen's chances of earning a point in St Petersburg.
"We still believed we could equalise but there was a third CSKA goal in a situation which cannot be predicted," Vrba said.
"Our second goal came too late.
"Sadly our own mistakes brought about the result."
|Coach: L. Slutsky|
for S. Zuber 64'
for R. Elm 73'
for A. Musa 89'
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