Diego Simeone's side came into the fixture on the back of six consecutive wins in the league and although Real started well, the visitors took the lead in the 11th minute through Diego Costa.
Real reacted at half-time by bringing Gareth Bale on for his home debut, but the world’s most expensive player could not make a difference as Atletico held on for three points to move level with Barcelona again as they continue to assert their early claim as genuine title contenders.
Real went into the match as favourites given their impressive record in the Madrid derby, but coach Carlo Ancelotti acknowledged the visitors’ attacking threat by replacing Luka Modric with the more defensive-minded Asier Illarramendi.
Simeone made three changes to the Atletico team that beat Osasuna 2-1.
Emiliano Insua, Leo Baptistao and the injured Mario Suarez missed out at the Bernabeu, with Filipe Luis, David Villa and Gabi taking their respective places.
The hosts looked to impose themselves early on, but Atletico took the lead just 11 minutes in.
Koke flicked a magnificent pass between Alvaro Arbeloa and Pepe, allowing Costa to surge into the area and coolly stroke the ball into the bottom corner for his eighth league goal.
Karim Benzema went close just past the half-hour mark as he connected with right-wing cross, but he nodded wide of the mark, before Tiago inexplicably headed over when unmarked.
A few moments before half-time, Diego Godin had a header stopped by Diego Lopez before Costa attempted to knock in the loose rebound, much to the goalkeeper's displeasure, as he exchanged words with the forward.
Ancelotti responded at half-time by replacing Illarramendi and Angel di Maria with Modric and Bale, with the latter making his first appearance at the Bernabeu since his world record transfer from Tottenham.
The controversial Costa found himself in trouble again early in the second period as he received a yellow card for dissent and he was lucky to escape a red card as he continued his argument.
Just after the hour mark, Costa was put through on goal by Villa, but after failing to get the ball out of his feet, he hit a shot straight at the grateful Lopez.
With 20 minutes to salvage a result, the quiet Cristiano Ronaldo had an effort from the left spilled by Thibaut Courtois and a few seconds later, Modric fired a volley just wide of the top corner.
Koke nearly rounded off a good display in the final 10 minutes as he curled a shot towards goal, but his effort flew back off the crossbar before Courtois palmed away a Bale scissor-kick at the other end to confirm victory.
