A bright start saw the Liga leaders take a deserved lead courtesy of Raul Garcia's 14th-minute header, which proved decisive in a game of precious few chances.
Jeremy Perbet nearly found an equaliser midway through the second half with a curling effort, but could only find the roof of the net.
Atletico's preparations for the game were affected by the hamstring injury sustained by Diego Costa in the 1-1 UEFA Champions League quarter-final draw at Barcelona in midweek, and they struggled to find their usual incisiveness in the final third in the absence of their top scorer.
However, a combination of Garcia's ninth Liga goal of the season and typically dogged defensive resistance secured a vital three points for Diego Simeone's side.
The win continues Atletico's unbeaten league run at the Vicente Calderon, which now stands at 18 games, and leaves them four points ahead of Barca at the top of the table ahead of the reigning champions' clash with Real Betis later on Saturday.
Simeone's men struggled to build on their early advantage, though, with the hosts' attacking threat noticeably weakened without Costa, who has scored 33 goals in all competitions this term.
However, Atletico’s resilient defence - the best in La Liga, having conceded just 22 times in 32 outings - restricted Villarreal's creative freedom in the final third for much of first half.
Perbet did manage to get behind the hosts' defence after 32 minutes, but his flashed ball across the box eluded both Trigueros and Cani.
