Trailing to Abraham Paz's header early in the second half, Almeria had looked to be heading for yet another defeat.
However, they hit back through Sofiane Feghouli in the 70th minute before Modeste M'Bami's winner moments later.
A dull opening was briefly punctuated by Paz's shot which Almeria goalkeeper Diego Alves caught in the seventh minute.
Cristian and Tote both had further speculative efforts for Hercules which failed to trouble Alves after Olivier Thomert had headed wide of the goal.
The game was brightening and after Almeria winger Albert Crusat's shot was saved easily by Juan Calatayud, Thomert was just wide with another header, this time from Francisco Farinos' corner.
Tote's cross found Abel Aguilar in the 30th minute as he headed wide in another example of the home side's profligacy.
Fabian Vargas forced the best save up to that point in the 34th minute as Calatayud had to dive smartly to tip his 12-yard shot round the post before, at the other end, Thomert could not connect fully with a loose ball.
Kalu Uche blasted wide for Almeria as the half petered out.
Just six minutes into the second half, though, the first goal arrived. After Hercules' Tote was fouled by Hernan Bernadello, Farinos' free-kick from the right found Paz who out-jumped the Almeria defence to nod home from six yards.
Almeria were stunned and Hercules could have gone further in front through David Trezeguet had he not fired over from 12 yards.
Having shown so little attacking nous, Almeria turned the game on its head in the space of three minutes.
In the 70th minute they restored parity when Crusat's cross was met by Feghouli, who ghosted in to convert expertly with his left foot.
Three minutes later they were ahead. Henok Goitom crossed from the left and again Hercules were flat footed as M'Bami blasted home with his right boot.
Hercules were stunned and made little inroads in the remaining 17 minutes as the Andalusians escaped with a precious three points.