Ikechukwu Uche scored the opening goal in the third minute with Bruno Soriano making sure of the win with a late penalty after Jonathan Pereira was brought down by Rafita.
The result means Villarreal leapfrogged Athletic Bilbao into the Champions League qualifying spot, although the Biscay club are yet to play this weekend and will host Real Valladolid on Monday.
Almeria, meanwhile, missed the chance to move clear of the bottom three, instead remaining in 17th place, just three points clear.
Villarreal got the match off to the perfect start for the home fans when they claimed an early lead thanks to striker Uche.
The Nigeria international fired home with just over two and a half minutes on the clock from within the six-yard box after he got onto the end of Giovani dos Santos' ball from the right.
After the dream start, Villarreal struggled to create many more chances, with Almeriaalso lacking any real creativity up front
Soriano blazed a shot over the bar before Almeria's Marcos Tebar had a shot blocked by Villarreal goalkeeper Sergio Asenjo before Alex Vidal was denied by Mateo Musacchio.
After the break, Marco Torsiglieri had a chance blocked by Villarreal midfielder Javier Aquino and the second half looked set to yield no more goals until Soriano's penalty three minutes before the final whistle killed off the game and give the home side the points.