The score on the night means that the two sides are currently locked at 3-3 on aggregate.
Madrid were awarded a penalty after only four minutes when David Alaba was adjudged to have handled in the area. Cristiano Ronaldo calmly slotted the ball past Manuel Neuer to put his side ahead.
Alaba almost made amends minutes later when he crossed for Arjen Robben, but the Dutchman somehow put the ball over from six yards.
Munich were on the attack soon after as Mario Gomez's stinging effort was pushed away by Iker Casillas into the path of Franck Ribery, who put the rebound wide.
The hosts were 2-0 in front on the night after 14 minutes when Ronaldo fired past Neuer following Mesut Ozil's pass.
Despite Madrid's lead, Bayern continued to pose a threat on the break as demonstrated when Gomez fired wide.
The Germans levelled the aggregate scores on 26 minutes when Robben squeezed the ball past Casillas from the penalty spot after Pepe had dragged down Gomez when challenging for the ball.
Gomez could have done better when he fired straight at Casillas shortly after, while Ronaldo tried his luck again from a free kick that was gathered by Neuer.
There was one last chance of the half for Robben, but his free kick was parried away by Casillas.
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