The hosts, who have also beaten Barcelona and King's Cup holders Sevilla this season, rattled in four first-half goals through Tote, Nelson Valdez, Olivier Thomert and David Trezeguet.
Atletico salvaged a little pride with a solo effort from Jose Antonio Reyes in the final minute, but the defeat left them seven points adrift of the top four in sixth with 27 points from 18 games.
Barcelona top the standings with 49 points, two ahead of Real Madrid after both won over the weekend.
Hercules quickly took the lead when Tote made the most of hesitant defending to shoot at the near post and Atletico goalkeeper David de Gea fumbled the ball into his own net after 11 minutes.
With Atletico's defence in disarray, Valdez broke across the edge of the area and curled a stunning shot into the top corner and Thomert glanced in a header to make it 3-0 in the 32nd.
Trezeguet's superb first-time shot sent Hercules into the break with a four-goal advantage which they never looked like relinquishing.
Sergio Aguero hit the post from a free-kick and Valdez crashed a shot against the post at the other end, but Atletico, who visit city rivals Real Madrid in a King's Cup quarter-final first leg on Thursday, failed to respond until Reyes struck.
Hercules climbed to 11th with 22 points.
