Jose Molina was taking charge of Villarreal for the first time and his side made an ideal start as Marco Ruben and Gonzalo had them 2-0 up inside 18 minutes.
But Sofiane Feghouli finished well at the end of an excellent team move to get one back before half-time and Villarreal were made to pay for passing up chances to kill the game off in the second half as Aduriz calmly curled the ball home from 18 yards.
Villarreal's struggles so far this season have in a large part been down to their inability to score goals, but with Nilmar and Ruben paired together up front they looked a far more potent threat in the final third.
And it was the two South Americans who combined for the opener after 14 minutes as Ruben bundled his way through a number of weak Valencia challenges before exchanging passes with Nilmar and calmly lofting the ball over Diego Alves.
However, if the first goal was down to inventive play from the hosts, their second minutes later owed a lot more to poor defending.
Gonzalo was left completely unmarked by Mehmet Topal six yards out to head home Borja Valero's free-kick.
Valencia were understandably shocked by their awful start to the game, but they slowly started to get back into the match and got their reward when Feghouli headed home Miguel's excellent volleyed cross.
The momentum was now with the visitors and they could have been level just after the break, but Roberto Soldado had an effort ruled out for offside before sending another effort narrowly wide from the edge of the box.
Alves then had to produce two fine saves from Borja and Nilmar to keep his side in the game and those stops proved to be decisive as substitute Aduriz collected Cristian Zapata's poor clearance just outside the box and passed the ball into the far corner after 87 minutes.
That goal kept Villarreal in the relegation zone, while Valencia extended their advantage over Levante in third place to four points.