The Yellows, who were without a head coach for this one, with Marcelino not set to be appointed until Monday, but they still managed to take the lead through Gerard Moreno.
The Spaniard turned home a rebound with a clever finish after Alexander Sorloth forced a save. Sorloth could have made it two not too long after, but he saw an effort saved by Jan Oblak.
Villarreal held on until stoppage time of the first half, when Axel Witsel latched onto the a cross the back post.
The Yellows stood strong in the second half, clearly hoping to take a point home from the capital, but their resolve was broken when a clever ball to the far post found Marcos Llorente, who delivered the perfect pass across goal at the first time of asking for Antoine Griezmann to tap home from close range.
Before Villarreal could truly chase the game, and just five minutes after the third goal of the game, Atletico made it 3-1 when Pablo Barrios sprinted through down the right-hand side of the box before crossing for Lino to produce a superb first-time finish.
That was that and Villarreal head into the international break 10 points off the top six, albeit they will have a new head coach by the time they return. The Yellows will also hope to get Alexander Sorloth back from injury after he limped off during the game.