Nelson Valdez and David Trezeguet scored to give the Alicante-based hosts a 2-1 lead at the break, after Joan Capdevila had equalised for the visitors.
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Promoted Hercules were reduced to 10 men when Trezeguet was sent off just before the interval and, after Borja Valero had levelled in the second half, Villarreal had two players sent off in the closing stages.
Villarreal climbed to second in La Liga with 16 points, one short of unbeaten leaders Real Madrid after seven matches, and are ahead of champions Barcelona and Valencia on goal difference.
Paraguay striker Valdez arrived in the area unmarked to score after a free-kick in the 26th minute but Villarreal levelled almost immediately when Spain defender Capdevila stroked home from close range.
A typically opportunist strike from former France striker Trezeguet put the hosts ahead again in the 41st but he spoiled the moment soon afterwards, earning himself a red card for something he said to the referee.
Villarreal were chasing a sixth consecutive victory and after twice hitting the woodwork in the first half, continued to press forward.
Spain midfielder Santi Cazorla set up Valero to level in the 63rd but with both sides piling forward at every opportunity Villarreal lost their cool.
Valero was sent off in the 81st minute for a second yellow card offence, and he was quickly followed down the tunnel by Argentine team-mate Mateo Musacchio.
Hercules, who have already beaten Barcelona and Sevilla since returning to the top flight, almost snatched a victory at the end, with Villarreal goalkeeper Diego Lopez saving twice in the frantic final minutes.
