Álvaro Morata scored twice and Antoine Griezmann once to hand Madrid their first loss after six straight victories in all competitions this season. Toni Kroos scored the lone goal for the visitors.
The result left Catalan clubs Barcelona and Girona at the top of the standings with 16 points each from six matches. Defending champions Barcelona rallied late to defeat Celta Vigo 3-2 on Saturday, while Girona beat Mallorca 5-3.
Madrid stayed one point behind in third place. They had won five consecutive league games, and on Wednesday beat Union Berlin in the group stage of the Champions League.
Atletico were coming off a 3-0 loss at Valencia for their first defeat of the season. Diego Simeone's team had two wins and a draw in their other previous matches.
All three goals by Atletico on Sunday at Metropolitano stadium came from headers. Morata scored in the fourth and 46th minutes, while Griezmann got on the board in the 18th. Madrid's goal came in the 35th after Kroos cleared a defender before finding the net from outside the area.
Madrid had a goal disallowed for offside in the 44th.
Coach Carlo Ancelotti couldn't count on Vinícius Júnior, who was set to return from injury but was dropped from the squad at the last minute because of a stomach illness.
Real Sociedad beat Getafe 4-3 at home with Japanese forward Takefusa Kubo scoring the opening goal for the hosts two minutes into the match, and Villarreal drew 1-1 at Rayo Vallecano with the teams scoring the goals a minute apart early in the first half.
Also Sunday, 10-man Las Palmas picked up their first win by defeating visiting Granada 1-0 with a stoppage-time goal by Kirian Rodríguez, and Real Betis drew 1-1 with Cadiz at home.
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