Atletico upsets city rival Real Madrid
On-form Diego Costa struck in the 11th minute and not even Gareth Bale in his home debut for Madrid could help it rally.
Atletico's big win came after Lionel Messi scored before being substituted due to injury to help Barcelona win 2-0 at Almeria.
Barcelona and Atletico set club records by staying perfect through seven rounds to start the season, opening up a five-point gap over Madrid.
Messi and Diego Costa lead the league with eight goals each.
Atletico's last league win against Madrid came in 1999, and since then it had gone 23 games without a victory.
Bale, Madrid's 100-million-euro man, went on at the start of the second half, finally playing in front of his new home fans after straining his left thigh while warming up before last weekend's match.
But neither the Wales winger in 45 minutes nor Cristiano Ronaldo in 90 were able to target Atletico's goal.
Atletico couldn't have asked for a better showing at the same Santiago Bernabeu Stadium where it beat Madrid last May to claim the Copa del Rey.
While Atletico squeaked out that cup win in extra time, Diego Simeone's side simply outplayed Madrid on Saturday, creating many more shots and deploying a swarming defense that kept Madrid in check until the final minutes.
Simeone pumped both fists on the final whistle as he left the dugout, deservedly satisfied with his team's effort.
Diego Costa, who also scored in last season's cup final, took the game's sole goal when Filipe Luis stole the ball from Madrid's Angel Di Maria and Jorge ''Koke'' Resurreccion placed a throughball for his goalscorer to coolly fire it in.
As the Brazilian forward soaked up the dismay of Madrid's supporters, Madrid coach Carlo Ancelotti turned away and slapped his leg in frustration.
Madrid was fortunate not to go into halftime down by another goal.
Atletico midfielder Tiago Cardoso squandered a great chance to double the lead in the 29th when he arrived unmarked to the area on a corner kick, only to send the ball well high.
Madrid goalkeeper Diego Lopez then made back-to-back saves to deny Diego Godin's header and Diego Costa's attempt to poke in the rebound in the 42nd.
Lopez bailed out Madrid again in the 61st when he bettered Diego Costa one-on-one on the break.
With both teams visibly tiring, Koke almost sealed the win in the 81st with a shot off the crossbar.
Three minutes later substitute Alvaro Morata drew a save from goalkeeper Thibaut Courtois in Madrid's best chance of the night before he hit the side netting in the 90th.
Messi netted his goal in the 21st minute with a left-footed shot after combining with Pedro Rodriguez, but he asked to be replaced eight minutes later after hurting a muscle in his right leg.
Adriano sealed the result in the 56th from a pass by Cesc Fabregas while Messi watched from the bench.
Messi's injury leaves him in doubt for Tuesday's Champions League match at Celtic, when Atletico plays at Porto. Madrid hosts Copenhagen on Wednesday.
Barcelona said the Argentina forward would undergo more tests on Sunday.
While Barcelona may be missing Messi for the trip to Glasgow, it should have Neymar well rested after the striker didn't play a minute at Juegos Mediterraneos Stadium.
Barcelona's first-year coach Gerardo Martino has guided Barcelona to its best start in 82 leagues. Five other managers, including Pep Guardiola (2009-10) and predecessor Tito Vilanova (2012-13), had reached six wins.
''I have only latched on to one of the records that these players have broken and continue to break,'' said Martino. ''They have been doing so for years both individually and as a team. The fact that I formed a part of this one is circumstantial.''