Raul Garcia headed in a first-half corner to give Los Rojiblancos the points in a game that saw both sides struggle to carve out anything clear cut.
Villarreal were marginally better in the second half to set up a tense few moments late on for the home side before they eventually held on for the win.
Here, Sports Mole analyses the win, as Diego Simeone's men maintained their title charge.
On target: 3
On target: 1
Was the result fair?
Probably not. Atletico Madrid claimed an early goal and then game was played almost at an exhibition's pace, with neither side doing anything of note. Villarreal were really poor in the first half and were only marginally better in the second. Atletico had their goal and were content to see it out. They did little themselves and really missed Diego Costa. A draw would have been a fairer reflection.
Atletico Madrid's performance
They did enough to extend their advantage at the top of the table and at this stage of the season, that is a valuable commodity. They were not at their best, missed Costa and struggled to carve out anything in front of goal. However, three points cannot be sniffed at.
Really poor from an attacking point of view. Defensively, they did well largely, but they never looked like they thought they could get back into the game after going a goal down. In truth, the game was drab.
Sports Mole's man of the match
Difficult to choose really with the kind of game it was, but Raul Garcia did well in the middle of the park. However, I'd have to plump for Felipe Luis. The left-back was a consistent threat down the flank and played some inviting crosses. A solid game from the defender.
Villarreal's attacking display was woeful from start to finish. Jeremy Perbet worked hard, but they never looked like they wanted to support him up top. Atletico weren't at their best and if Villarreal believed a bit more, they might have had an equaliser. A poor display from the creative players in yellow.
There were four bookings in total, and all were probably correct. There were no major decisions for the official to make, and he was largely anonymous - apart from when he was struck with the ball to break up an Atletico attack. A quiet performance from the referee, normally indicates a good one.
Atletico Madrid: Los Rojiblancos host Barcelona in the Champions League in midweek, before another home game to Getafe.
Villarreal: The Yellow Submarine host Levante next Sunday.