Almeria out of King's Cup
Hugo Sanchez's team had a chance to level the tie on home soil when Pablo Piatti won a penalty in the 55th minute but the Argentine striker's weak spot kick was easily saved by Hercules goalkeeper Unai Alba low to his left.
Piatti's compatriot Hernan Pellerano headed against the bar nine minutes later but Almeria's chances were effectively snuffed out after 76 minutes when Tiago Gomes timed his run perfectly to meet Cristian's cross and volley past Esteban.
Almeria's misery was compounded in added time when Pellerano was dismissed after picking up a second yellow card.
By far the biggest shock of the round came on Tuesday when Real Madrid were dumped out 4-1 on aggregate by lowly Alcorcon, the second year in a row the La Liga giants have been eliminated by a side from the third tier of Spanish football (Segunda B).
Last year's finalists Athletic Bilbao lost 4-2 to second division Rayo Vallecano over two legs and La Liga sides Sporting Gijon and Tenerife were also eliminated by second tier clubs.