Nacho's first-half opener for the hosts had been cancelled out by former Madrid midfielder Wesley Sneijder early in the second period.
However, Madrid weren't to be denied victory in the friendly held to celebrate the Santiago Bernabeu trophy thanks to Marcelo's strike eight minutes from time.
Benitez named close to his strongest available line-up just five days before Los Blancos kick-off their La Liga campaign away to Sporting Gijon.
However, it was a less than convincing start from the hosts as Umut Bulut headed just wide before Lukas Podolski forced Keylor Navas into his first save of a busy evening.
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Isco was inches away from doubling Real's advantage with a lovely curling effort that clipped the bar before Bulut passed up a great chance to equalise when he blazed over from barely three yards out.
Gareth Bale endured another largely frustrating night as he too failed to find the target with an effort from distance and was met with boos from sections of the home support.
And even Cristiano Ronaldo's eye for goal wasn't in as the World Player of the Year spooned a glorious opportunity over from Jese Rodriguez's fine cut-back with the last action of the first-half.
Navas saved Benitez the embarrassment of going behind on his home debut with a stunning save from Sabri Sarioglu moments later.
Both sides then made a raft of substitutions, but there was one moment of real quality left to decide the game as Marcelo skipped past three Galatasaray defenders before prodding the ball home at the near post.