The defeat left the Yellow Submarine in seventh position in La Liga - 10 points from the top four - but Marcelino offered no excuses following the clash at the Mestalla.
"The best team won over the ninety minutes and we must congratulate them. They were more intense and got forward better," he told reporters at a press conference.
"They made the most of two set-pieces where we were very permissive. The fruits of their superiority in the first half took the game where they wanted it and although it was more even in the second half, we couldn't create enough danger. It's a fair result for them."
Villarreal have lost 10 times in the league this season.