Real were first out the blocks in the second half, as Benzema capitalised on a awful mistake from Sven Ulreich to bag his second of the night and put Madrid back in control.
Bayern still created chances before and after Rodriguez's goal. Zinedine Zidane's side took a 2-1 lead into the second-leg against Bayern Munich, but it wasn't an easy night at the Bernabeu.
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Benzema replied in the 10th minute with his opening goal before scoring again in the 46th minute to give Madrid a 4-2 buffer on aggregate. The Frenchman was set up on a lovely assist from left-back Marcelo, who dropped it right in front of goal.
Joshua Kimmich scored for Bayern in the third minute to set the stage for another comeback at the Santiago Bernabeu, like the one Juventus almost pulled off in the quarterfinals. Lewandowski's shot was saved by Keylor Navas, and the ball popped high into the air across the face of goal, and came down on the head of Muller, but that effort was blocked.
Controversy came right before the half when it appeared that Marcelo got his hand on a ball in the box. James was finally able to score against his former team and the club that still owns him in the 63rd minute when his first try was deflected but he successfully crossed back the rebound past Navas.
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James almost got his second goal about ten minutes later as he wound up at the top of the goal, but defender Raphael Varane made an important stop by throwing his body in front of James' attempt. Cristiano Ronaldo could have wrapped it up from Marcelo's cross as Madrid looked to finish it off; instead James Rodríguez drilled past Navas at the second attempt to revive Bayern hopes, but Madrid held on in a frenetic final half-hour.
Anything less than a victory tonight will see the Bundesliga champions firmly extinguished from this season's Champions League.
Following the mistake, Bayern pushed forward knowing they needed two goals to advance.
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Real Madrid will await the victor of the Roma - Liverpool series that the English side now leads 5-2 heading into Wednesday's second leg.