A pulsating first half saw Villarreal go two goals up inside the opening 15 minutes.
Alberto Moleiro scored a season-high seventh league goal after he was released by Georges Mikautadze, sending the ball into the far bottom corner.
The provider then got on the scoresheet himself as he produced a similar finish after being found by Nicolas Pepe.
However, Elche halved the deficit after the half-hour mark as Aleix Febas fed Martim Neto, who turned and shot brilliantly into the far corner from the edge of the box.
Both teams had further chances to score before half-time too, as Ayoze Perez’s strike was well-saved by Inaki Pena, before Neto came close to netting again with a diving header that flew just over.
Mikautadze had the chance to make sure of the points early in the second half as he was sent through on goal again, but this time he tried to be a bit too clever as he chipped the ball onto the roof of the net.
Elche threatened to punish that miss but were unable to find the leveller, as Alfonso Pedraza bundled home in the latter stages after latching onto a wonderful long pass from Sergi Cardona to seal victory and end a run of three straight defeats.
The Yellow Submarine are now third in the table as a result, while Elche drop to ninth after being denied what would have been back-to-back wins for the first time this season.
Flashscore Man of the Match: Georges Mikautadze (Villarreal)