Cristiano Ronaldo's 25th league goal of the season was the difference between the two sides at La Rosaleda, as Carlo Ancelotti's men continued to set the pace at the La Liga summit ahead of El Clasico against Barcelona next weekend.
After falling to a surprising 3-2 loss at Malaga last season, Real looked determined to avoid a repeat this year.
But they were still made to work hard for the win, which came via Ronaldo's precise finish in the 23rd minute, as he fired into the bottom-right corner.
The Ballon d'Or winner could have made it more comfortable when he headed narrowly wide just prior to the break, but this time he missed the target.
That ended Almeria's hopes of a comeback as Rayo moved three points ahead of their 19th-placed visitors.
Celta Vigo opened up a healthy gap between themselves and the bottom three thanks to a valuable 1-0 win at Levante in Saturday's early kick-off.
Nolito's back-post tap-in from Augusto Fernandez's cross was enough for the visitors as David Barral missed his 61st-minute penalty for Levante.
