Cristiano Ronaldo had given the visiting Spaniards a deserved 1-0 lead after 28 minutes, taking full advantage of a CSKA defensive mix-up and beating nervous-looking goalkeeper Sergei Chepchugov with a low volley into the far corner.
It was Ronaldo's 17th goal in his 23rd Champions League game for Real and 32nd in total in Europe's premier club competition.
The Portugal striker missed a chance to double the lead shortly after the restart, but this time Chepchugov, making his Champions League debut, averted the danger.
Ronaldo had another opportunity late in the game but fired just wide of the post with a low shot from the edge of the box.
The nine-times European champions dominated for most of the match despite playing in sub-zero temperatures on Luzhniki's unfamiliar artificial pitch but paid dearly for their misses when Sweden midfielder Wernbloom equalised in the last minute of added time following a disputed free-kick.
Real coach Jose Mourinho blamed Dutch referee Bjorn Kuipers for the CSKA goal.
"I'm disappointed with the result. We should have scored the second goal, then we would have won for sure," the outspoken Portuguese told Russian television NTV Plus.
But that free-kick near the end of the game should have been taken in the opposite direction," he added.
"I must give credit to CSKA as they fought until the end, but the referee had allowed them to play very aggressively and didn't show them any yellow cards."
The home side sorely missed their first-choice goalkeeper Igor Akinfeyev, who is still recovering following knee surgery.
Chepchugov made a fine double save early on, first stopping Gonzalo Higuain, who had just replaced injured Karim Benzema, then denying Sami Khedira from close range seconds later.
The visitors lost France forward Benzema just 15 minutes into the game after he appeared to pull a muscle while taking his first shot on goal.
CSKA's Ivory Coast striker Seydou Doumbia, who has scored five goals in five Champions League games this season, was kept off the ball for most of the match by Real's tight defence.
The Russians struggled to create much of the offence until Wernbloom, who joined CSKA in January, beat Iker Casillas from 10 metres following a goal-mouth scramble with virtually the last kick of the game, sending a record 70,000-strong home crowd wild.
"We made a silly mistake in the first half and they punished us. But in the second half we had some extra attackers pushing forward and probably that was the key," said CSKA coach Leonid Slutsky.
"We only had a few chances without playing particularly well but were able to get a goal in the end.
"I think Real are still the favourites but for us anything is possible."
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