Cristiano Ronaldo and Real Madrid had plenty of opportunities to score vs. Villarreal, but the Portuguese star's goal from the penalty spot was all the team could manage in their 1-1 draw.
Villarreal threatened early, but a Gerard Moreno attempt from point blank was saved by Iker Casillas and the rebound attempt by Moi Gomez was headed off the line by Dani Carvajal.
Both sides missed out during a flurry of late chances in the game's closing 15 minutes. The win leaves Real Madrid just two points ahead of Barcelona in the race for the La Liga season title.
Atletico Madrid's hopes of retaining the Primera Division title are all but gone after drawing 0-0 at Sevilla.
Diego Simeone's side were pinned back for much of the game and were fortunate to go into the break on level terms, although they improved in the second half and had a couple of chances to snatch a late winner.
The result sees Atletico drift five points behind second-place Barcelona and even further behind league leaders Real Madrid in La Liga table, their emphatic 4-0 victory over their local rivals three weeks ago now a distant memory.
Sevilla's hopes of catching Valencia in the final Champions League spot were also dented by the draw, and they fall seven points behind fourth spot.
A quick-fire double from Pablo Piatti earned Valencia a 2-0 win at home to Real Sociedad and continued their push for the fourth Champions League place.
The Argentine forward broke the deadlock in a tight match eight minutes into the second half and scored again moments later to put Nuno Espirito Santo's side on to 53 points, their best total at this stage in a season since they won the Primera Division title in 2004.
David Moyes' men, though, remained five points away from the drop zone.
Athletic Bilbao stretched their unbeaten run to three matches by edging out Eibar 1-0 on Sunday.
Carlos Gurpegi's first-half goal was all that separated the sides, although the visitors could have a hatful at the Ipurua Municipal Stadium but for a fine performance from home goalkeeper Jaime Jimenez.
The win nevertheless lifts Athletic above their opponents, who have now lost six on the trot as they continue to slide down the table.