Kevin Volland put Leverkusen ahead after 16 minutes before Israeli international Bibras Natcho converted a second-half penalty to snatch a draw for the Russian club.
Leverkusen will be assured of qualifying if Monaco beat English club Tottenham in Group E later Tuesday.
Bayer manager Roger Schmidt said he was pleased with a point.
"It was a very intense match," he told a news conference.
"I'm pleased that I made clear the importance of this match to my men and we looked really well in the first half. We opened the scoring and had chances to increase our lead.
"But in the second half CSKA picked up steam and reversed the situation to pull the scores level. Hopefully, later today we will be able to find out how precious was the point that we've gained here."
The visitors started in a lively fashion and in the eighth minute Hakan Calhanoglu squandered a chance for an opener sending the ball inches wide off the far left post with an angled low shot.
CSKA replied with a shot by Alexander Golovin from the edge of the six-yard box, which was confidently denied by Bernd Leno.
In the 16th minute Volland made CSKA pay for loss of concentration as he escaped an offside trap to latch on to a razor-sharp pass by Kevin Kampl, who fired the ball home from eight yards out past helpless 'keeper Igor Akinfeev.
Alan Dzagoev, who has returned after two months out with injury, missed an opportunity to level just before the half-hour mark as his seven-yard volley flew just over the crossbar.
Bayer skipper Omer Toprak also sent the ball into the net in the 39th minute but his goal was rightly ruled out for offside.
After the break CSKA, who needed to win to keep alive their hopes for a place in the knockout stages, poured forwards and in the 69th minute Alexander Golovin failed to score from a rebound from just four yards out.
But in the 76th minute Natcho pulled level from the spot after Bayer back Benjamin Henrichs fouled Mario Fernandes in the box.
Volland could have restored the visitors' lead with 10 minutes to go but his curling close-range effort hit the woodwork and bounced back into play.