The January signing volleyed home with seconds remaining to send the stadium into raptures and deny Jose Mourinho's men, who looked certain to take a lead back to Santiago Bernabeu for the second leg.
The hosts, amidst freezing conditions in the Russian capital, made a positive start to the match, with Seydou Doumbia and Ahmed Musa looking dangerous. Their electric pace and dribbling ability was obvious, but no clear-cut chances were created and Madrid began to impose themselves on the game.
The ascendancy of the visitors stalled slightly, though, due to an injury to Karim Benzema a quarter of an hour into play. The Frenchman went down innocuously and had to be withdrawn due to what appeared to be a groin problem.
Mourinho's side then had a great chance to take the lead but were denied by a terrific double save from Sergey Chepchugov. Gonzalo Higuain, Benzema's replacement, latched onto a loose ball just outside the box and lashed a left-footed shot at goal that was palmed away by the CSKA goalkeeper, who got up instantly to tip Sami Khedira's rebound over the bar.
The breakthrough did eventually come for Real Madrid, through good work from Portuguese pair Ronaldo and Fabio Coentrao.
The left-back found himself in an advanced position down the wing and whipped a cross to the back post which proved too much for Zoran Tosic, who awkwardly headed the ball into the path of Ronaldo. The Madrid talisman showed great composure to drill a left-footed half-volley at goal, which squeezed past the glove of Chepchugov.
The second half saw the Real Madrid defence looking relatively comfortable, as the hosts struggled to break through a solid back line.
Chances were at a premium, but the Spanish outfit had an excellent opportunity to double their lead in the 75th minute and it took another good save from Chepchugov kept his side in the match. Ronaldo broke the CSKA offside trap and ran through on goal attempting to take the ball around the goalkeeper, who remained big to make an important block.
Ronaldo again should have doubled his tally seven minutes from time when he found himself with plenty of space on the edge of the box, but dragged his shot wide of the left-hand post.
The win looked to be in the bag for Real Madrid, but CSKA had other ideas. In the last minute of injury time, Alexey Berezutski got on the end of a deep cross to head the ball back into the danger area of the Madrid box, and Wernbloom was there to smash home from seven yards.
The tie between CSKA Moscow and Real Madrid is perfectly poised for the second leg two weeks from now at Santiago Bernabeu, and although the hosts will certainly be buoyed by the manner of their equaliser, the Spanish still hold the advantage of a precious away goal.