Antonio Rudiger and Aurelien Tchouameni made their first starts in a Los Blancos jersey, while the likes of Luka Modric, David Alaba and Casemiro started on the bench following their involvement in Wednesday's UEFA Super Cup triumph.
The home side got off to the perfect start when Inigo Eguaras' first-time ball sent Largie Ramanzani through on goal and the striker duly fired past Thibaut Courtois.
Federico Valverde went close to bringing the visitors level in the 16th minute, with Uruguayan midfielder forcing a smart save out of Fernando Martinez with an effort from the edge of the box.
Benzema, who need in the Super Cup, went close to pulling Los Blancos level with 28 minutes played but his header at the far post was saved by the Almeria shot-stopper.
The visitors thought they had secured the equaliser on the stroke of halftime when Lucas Vazquez turned home Kroos' strike, but celebrations were cut short due to the offside flag being raised.
With Los Blancos struggling to find a way past Martinez, who had denied Benzema and Valverde early in the second half, Carlo Ancelotti threw on Eden Hazard for Tchouaméni on the hour mark.
Martinez finally broke on 61 minutes when Benzema collected a cross from Vinicius Junior before picking out Vazquez, who poked the ball home from 10 yards out.
The visitors then went on to take the lead with 15 minutes through a moment of brilliance from substitute David Alaba, who curled home a free-kick just seconds after replacing Ferland Mendy.