The home side now sit 16th in the table on 30 points, while Almeria have dropped to 17th, just one point outside of the bottom three with seven games remaining.
Valladolid continued to dominate in the opening 20 minutes and came close twice more through Victor Perez and Manucho, but Almeria survived once more.
Almeria grew into the early stages of the second period and had another half-chance on 54 minutes when Aleix Vidal found space outside the box, but his effort moved just wide of the post.
The away side's challenge suffered in the latter stages, however, when Marco Torsiglieri picked up his second yellow card of the afternoon for a poor challenge on Manucho.
Moments later, Jeffren attempted an effort from distance for the home side, but it moved high and wide of the crossbar.
Daniel Larsson and Manucho both came close for Valladolid in the latter stages, but the pair could not add to the scoring as Valladolid secured all the points with a one-goal margin.