But Los Rojiblancos were made to sweat for the three points.
Captain for the day Raul Garcia headed in the only goal of the game after 14 minutes, but the hosts created few further opportunities and spent the latter stages holding on amid Villarreal pressure.
And they survived a scare in the final minute when Toby Alderweireld diverted a cross just inches wide of a post.
Atletico coach Diego Simeone cut a nervous, restless figure on the touchline and was relieved when the final whistle sounded, the win keeping his side ahead of title rivals Barcelona and Real Madrid whatever their results this weekend.
This hard fought triumph was Atletico's third consecutive 1-0 win at home in the league, highlighting both Simeone's team's resilience and his thin resources.
With top scorer Diego Costa and Arda Turan injured and captain Gabi suspended, Simeone had to pull together a makeshift side, giving starts to Cristian Rodriguez, Diego and Mario Suarez, while Alderweireld deputised for Miranda in defence.
Villarreal also had to deal with injury problems, with Mateo Musacchio, Giovani Dos Santos, Ikechukwu Uche and Jaume Costa all missing.
Diego had given Atleti the lead at Barcelona in midweek with a stunning goal and came close to putting them in front after four minutes, combining with Koke from a rehearsed corner, but putting the ball a couple of feet over.
Atletico, though, only had to wait another 10 minutes to score, Garcia appearing at the near post unmarked to nod in a Koke corner. Villarreal thought the goal should have been disallowed as Garcia had pushed Mario Gaspar in the back before heading in his ninth league goal of the season.
Villarreal had more of the ball, but were stifled by Atletico's defence, their best move a one-two between Cani and Manu Trigueros snuffed out by Diego Godin.
They grew into the game in the second half, making more incursions into Atletico's area. Cani shot wide then Jeremy Perbet tried to curl the ball into the far corner from the left hand side of the area, but could not steer his shot under the bar.
Atletico were unable to trouble Villarreal's backline after the break, their only attempts a soft effort by David Villa easily caught by Sergio Asenjo, a low shot from Garcia that the goalkeeper also gathered comfortably and a scuffed drive from substitute Tiago Mendes that went well wide.
And home hearts were in their mouths when Alderweireld's attempted clearance went across the face of the goal, but the Calderon breathed a huge sigh of relief as it dropped wide, leaving Simeone's side still in charge in the title race.