Fernando Tissone and Francisco Portillo were on target as Malaga made it four games without defeat after their sluggish start to the season.
Alex Vidal had the first chance for the visitors but he could only drag his speculative effort wide before Sergio Duda brought a save from Esteban Suarez down the other end.
The home side had their tails up in the early stages with Mounir El Hamdaoui the next to fire wide and Vitorino Antunes soon brought another save from Esteban.
Lozano Rodri should have fired the visitors ahead after 12 minutes but he somehow missed the target from six yards.
Duda tried a long-range effort just before the half-hour but Esteban was equal to it again as Malaga pushed for the opener their dominance would have merited.
But again Almeria came back as Marcos Nelson's shot from a corner brought a smart save from Willy Caballero.
El Hamdaoui, Duda and Bobley Anderson all tested Esteban before the break but Malaga could not find a goal to edge them ahead at half-time.
Malaga had been the better side but Almeria were not giving up and Angel Trujillo tested Willy in the early stages of the second half.
Suso had a further effort for the visitors but it was once again Malaga who went first to breaking the deadlock as El Hamdaoui hit the post from six yards out.
Sergi Darder then brought a stunning save from Esteban before Malaga at last took the lead through Tissone.
Duda provided the corner and when Sergio Sanchez headed across the box, Tissone was on hand to provide the finishing touch in the 69th minute.
Roque Santa Cruz was brought on as a late substitute and he provided the pass for Portillo to curl one home and seal the win.