Down 3-1, Napoli pushed for another goal but could not finding it, wasting a couple quality chances that could come back to haunt the side in the second leg.
The four-time Ballon d'or victor netted a fantastic free-kick as Madrid came from behind to beat Sporting 2-1 at the Santiago Bernabeu and then opened the scoring for Zinedine Zidane's side in Dortmund after 17 minutes in a 2-2 draw on September 27.
James Rodriguez was named in the Real Madrid starting XI for just the second time in 2017 ahead of Wednesday's Champions League last-16 first leg against Napoli.
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Real will feel good about this result, but that away goal means Napoli still has life.
Toni Kroos then gave Real Madrid the lead in the 49th minute after Cristiano Ronaldo beat his defender and set up the German for a low effort to the front post.
Napoli were looking confident and composed but they relaxed a little too much to allow Benzema to equalise 11 minutes later, the striker glancing a header into the net from six yards after Dani Carvajal was allowed time and space to the right of the area to produce a sublime outside-of-the-foot cross.
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Five minutes later, Real Madrid made it 3-1 on the night and it was a once-in-a-lifetime strike from Casemiro, who found the far corner of the net with a sensational volley from distance to put Napoli in all sorts of trouble.
It was a thoroughly dominant performance from Real after a shaky start, during which Lorenzo Insigne scored for Napoli just eight minutes in.
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