The visitors did have a good chance to take the lead midway through the first half when Javier Aquino's shot from the edge of the area flew wide of goal.
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Seconds earlier, the hosts almost had a goal when Daniel Larsson's right-footed drive from the edge of the area was inches wide of Asenjo's post.
Valladolid almost put daylight between themselves and a below-par Villarreal when another Rossi cross was met by Stefan Mitrovic and his header went narrowly past the post.
With 13 minutes remaining, Villarreal's best chance to get back on level terms went begging when Manu Trigueros's through-ball reached Ikechukwu Uche, but his shot was straight at Real keeper Diego Marino and the hosts were able to hang on for victory.
The result means that Villarreal remain outside the top four in the league table, while Valladolid's hopes of survival are boosted.