Barca and Atletico have both win all their Primera Division fixtures so far this season and boast a five-point lead over Real, who lie third.
At the Bernabeu, in-form striker Diego Costa struck in the 11th minute and that proved to be winner for Diego Simeone's men.
A mistake from Angel Di Maria left Madrid flat-footed and a quick pass from Koke behind the defence played in Costa.
As Madrid waited for an offside flag, Costa brought the ball under his control and guided a low 15-yard finish under Diego Lopez and across goal into the bottom right corner.
Gareth Bale came on in the second half but Real could not conjure up an equaliser and Koke almost doubled Atletico's advantage, only to see his shot come back off the bar.
Lionel Messi's eventful week continued as Barcelona won 2-0 at Almeria to make it seven wins from seven to start the league season.
Messi, who appeared in court on Friday to answer questions relating to tax evasion, opened the scoring but lasted only 28 minutes before being withdrawn due to a thigh injury, with the club later confirming he will undergo scans on Sunday.
In his absence, Adriano added a second goal in an unusually low-key win for the Spanish champions.
Valencia were nearly overcome by stage fright but a solitary goal from Jonas was enough to secure their third straight win and see off Rayo Vallecano 1-0.
Boss Miroslav Djukic was on thin ice after overseeing three straight La Liga defeats before watching his team lose 3-0 to Swansea at the Mestalla, but subsequent wins over Sevilla and Granada lifted them back into the top half.
They reached 12 points on Saturday thanks to a fortuitous 37th-minute goal from Jonas but, when Rayo came looking for an equaliser, Valencia were suddenly beset by nerves and only luck saw them cling onto all three points.
Sevilla's long wait for an away win in the Primera Division goes on as they were unable to hold on to a half-time lead and drew 1-1 at Real Sociedad.
Jairo Samperio's neat finish in the 18th minute put Sevilla on course for a first away victory in La Liga in 20 attempts but Sociedad hit back in the second half to draw level through Antoine Griezmann.