The Yellow Submarine climbed over Diego Simeone's side with a win on Monday, with Manu Trigueros, Jonathan dos Santos and Roberto Soriano finding the net.
Villarreal dealt Atletico Madrid's rapidly fading La Liga titles hopes another blow as they coasted to a comfortable 3-0 win at El Madrigal on Monday.
Atletico's uncharacteristic sloppiness at the back proved particularly damaging, with individual errors to blame for Villarreal's first-half goals and a third league defeat in five to leave Diego Simeone's men 12 points adrift of pacesetters Real Madrid.
Tiago was culpable for Villarreal's first goal with Manu Trigueros profiting and applying a calm finish, before a goalkeeping howler from Jan Oblak allowed Jonathan dos Santos to add the second before half-time.
Villarreal were less reluctant to commit players to attack in the second period, with their miserly defence standing up to their reputation as La Liga's best having conceded just 10 goals so far this season, but Roberto Soriano made sure of the points in the closing stages.
Atletico's front trio of Angel Correa, Kevin Gameiro and Antoine Griezmann - confirmed in third for the 2016 Ballon d'Or during the match - were starved of opportunities throughout, highlighting Villarreal's excellent display defensively.
Victory for Fran Escriba's side lifts them above Atletico and Real Sociedad to fourth, with the visitors seemingly facing a battle to even finish in the Champions League places this term.
Villarreal looked sharper from the offset, but Koke saw an effort from just inside the area deflect off Alvaro Gonzalez and hit the left-hand post in the 19th minute.
Atleti shot themselves in the foot just before the half-hour mark, though.
Tiago's pass to Diego Godin was under-hit and Trigueros pounced to steal the ball before steering a cool finish into the bottom-left corner, with the Atletico midfielder - showing no clear sign of injury - swiftly replaced by Saul Niguez.
Villarreal exploited another error to double their lead. Oblak, who was withdrawn before half-time due to injury, fumbled Alexandre Pato's cross allowing Dos Santos to prod home from close range.
The visitors perked up slightly after the break and Gameiro almost met Juanfran's teasing delivery in the 48th minute.
But Villarreal, clearly content with their two-goal lead, sat back to good effect and absorbed pressure well, with Atletico struggling to break down their stubborn defence despite dominating possession.
Villarreal's defensive repertoire was put to the test during the latter stages as they were forced to withstand an aerial bombardment from their desperate visitors.
But they stood up to the task well and ultimately finished Atletico off in stoppage time.
Soriano darted in from the right, squeezing between a couple of defenders before playing a one-two with Alfred N'Diaye and placing into the bottom-right corner to leave Simeone's men well-beaten.
