Manu Trigueros put the impressive hosts in front with a low finish after experienced midfielder Tiago gave the ball away with a weak back pass after 28 minutes, before Jonathan Dos Santos made it 2-0 ten minutes later by pouncing when keeper Jan Oblak spilled Alexandre Pato’s shot.
Both Tiago and Oblak were substituted off straight after their mistakes – Tiago for discomfort in his knee, but Oblak looked to have hurt his shoulder in the build up to the second when he tried to stop Dos Santos reaching the loose ball, and the club confirmed via their website that he was taken to hospital.
Atletico never looked like getting back into the game, and Villarreal deservedly scored a third when Roberto Soriano cut a scuffed effort into the far corner.
The Monday defeat sees the title hopes of Diego Simeone’s side fade as they fall 12 points behind La Liga leaders Real Madrid into sixth place and now have to target a top-four finish rather than a title push.
Villarreal meanwhile leapfrogged Atletico into fourth place with 26 points from 15 games.
‘The result does not reflect the story of the game but when you commit errors like the ones we made you end up paying for them,’ said Atletico captain Gabi after the visitors were beaten for the fourth time in seven league matches.
‘We need to improve so we can get back towards the top of the table.’