It was the visitors who carried the attacking threat in the first half and came close to breaking the deadlock as early as the sixth minute, with Diego Lopez having to palm away Jorge Molina's header.
The 31-year-old was the one who eventually opened the scoring, though not without a frightening turn of pace from Cedric Mabwati, who blazed a trail through the Los Blancos backline and served the ball on a plate.
Cedric continued to dazzle with another scintillating run down the left to set up Joan Verdu, who fired wide of the goal.
Karim Benzema nearly equalised in the 25th minute when his studs came within inches of connecting with Marcelo's driven cross, but the Frenchman did not have to wait too much longer to get his name on the scoresheet.
Just a minute later, Benzema slammed the ball past Stephan Andersen after a driving run into the box to the relief of the Santiago Bernabeu faithful.
Despite that setback, it was still the visitors who looked more of a danger, with Nosa Igiebor hitting the bar after connecting with Verdu's corner kick.
However, the Portuguese forward shot straight at keeper Stephan Andersen, who showed safe hands to keep his side level after 69 minutes.
As the match entered the final stages only one team looked likely to win, but when Angel di Maria spurned a decent opportunity in the 81st minute, the points seemed destined to be shared.
After all their positive play, the night was to end in defeat for Pepe Mel's team, as Isco glided onto the end of a Marcelo delivery to head the winner on his debut in a Los Blancos shirt.