However, the lead didn't last long as Juanfran gifted the visitors an equaliser when he chested Angel di Maria's cross into his own net in the 13th minute.
Atletico continued to look dangerous and predictably it was Falcao who once again came closest to scoring as he ghosted in at the back post before heading wide from close range.
The derby was played out in a typically competitive fashion but Real seemed to be missing the influence of Cristiano Ronaldo.
Karim Benzema should have put the visitors ahead before the break but he delayed his shot and goalkeeper Thibaut Courtois was able to make a good save at the feet of the striker.
Atletico enjoyed the better of possession early in the second half and Diego Costa was unlucky to see a powerful header crash against the crossbar.
Despite seeming to lack real threat in attack, Real took the lead against the run of play in the 63rd minute when Benzema picked out Di Maria, who beat Godin before drilling an effort into the bottom corner.
The hosts pushed for an equaliser as the game reached its climax but Filipe Luis wasted the best chance when he fired a half-volley into the side-netting, allowing Real to collect the three points.