The hosts had won both fixtures between the clubs in last season's Segunda Division, but Ikechukwu Uche struck in injury time to move Villarreal three points clear of Athletic Bilbao in the final UEFA Champions League spot.
Hernan Perez wasted two gilt-edged chances for the away side, with Giovani dos Santos the provider on each occassion.
Manu del Moral went closest for Elche, but his header from Fidel's cross cannoned back off the crossbar.
Villarreal attacked from the off after the break, but they were dealt a blow five minutes into the second half as Dos Santos was forced off with a groin injury.
Perez continued to threaten but was again off target, while Elche goalkeeper Manu Herrera was called into a stunning close-range stop as Bruno latched onto Cani's free-kick.
Bruna again called Herrera into action with a 20-yard free-kick as the game looked to be meandering towards a draw.
But Villarreal snatched the win as Jonathan Peireira's scuffed effort landed at the feet of Uche, who tucked home from an apparent offside position, although the flag was not raised to the hosts' chagrin.