The reigning champions began the contest without nine first-team players because of injury or suspension but were dominant throughout.
Karim Benzema headed in the opener before defender Ferland Mendy doubled the lead from a move he started.
Real now trail Atletico by five points but have played two games more.
With the likes of Eden Hazard, Sergio Ramos, Federico Valverde, Toni Kroos and Alvaro Odriozola all absent, Real boss Zinedine Zidane elected to field an unusual 3-4-3 formation.
And it worked perfectly against opponents who lacked ambition and have struggled for goals in the Spanish top flight this term.
Marvin Park, 20, provided an outlet on the right on his first start, and with the result secure Zidane handed a league debut to 20-year-old defender Victor Chust late on.