Nigerian forward Chukwueze hit a curled finish late on to leave Real 12 points behind leaders Barcelona, having played a game more.
The hosts had taken the lead through a Pau Torres own goal but Chukwueze slotted in an equalizer.
Vinicius Jr’s solo strike put Real ahead but Jose Luis Morales equalized before Chukwueze stunned the hosts.
With just 10 La Liga games remaining, Real would need a solid finish for the season and an unlikely Barcelona collapse to defend their title.
Real thought they had an opportunity for a late equalizer when they were awarded a penalty after the referee felt Aissa Mandi handled the ball as he fell to the ground inside his own box.
However, Javier Alberola Rojas overturned that decision after going to the pitchside monitor following a VAR review.
The win moves Villarreal to fifth in the table, four points off the top four.
Barcelona, meanwhile, could move 15 points clear at the top when they host Girona on Monday.
Source: (BBC Sport)
