Zinedine Zidane made a couple eyebrow-raising inclusions, with Mariano Diaz leading the attack while Martin Odegaard was also handed a start alongside Eden Hazard.
Los Blancos broke the deadlock as early as the second minute, with Mariano making his opporunity count by nodding home Dani Carvajal's cross.
The Yellow Submarine nearly found themselves level in the 23rd minute but Ferland Mendy popped up with a vital block to deny Trigueros in the box.
Zidane's charges saw most of the ball in the latter stages of the first half, but they had efforts no threatening efforts on target while Villarreal were unable to test Thibaut Courtois at the other end.
Los Blancos had the chance to extend their lead five minutes after the break, but Mariano fired over the crossbar from the edge of the box after being picked out by Lucas Vazquez.
Zidane the opted for a double change just after the hour mark, as Odegaard and Hazard made way for Vinicius Junior and Isco.
Villarreal were then awarded a penalty on 75 minutes after Courtois had brought down Samuel Chukuweze in the box, which allowed Gerard Moreno to level matters from 12 yards out.
In the end, Los Blancos showed no attacking threat to get a winning goal as they miss the chance to move level on points leaders Real Sociedad.
