Karim Benzema, Vinicius Junior, Luka Modric, Thibaut Courtois, Ferland Mendy and Dani Carvajal were all rested by Real following their win over Manchester City in the UEFA Champions League semi-finals.
However, the champions were fortunate not to concede inside three minutes when a low shot on the far side of the area by Angel Correa rolled narrowly beyond the bottom-corner.
The host - backed by a lively crowd - took the lead eight minutes to halftime when the Video Assistant Referee (VAR) saw Matheus Cunha succumb to a challenge in the area and a penalty followed.
It was then left to the Belgian Yannick Carrasco to do the honours and he didn’t disappoint as he sent Andriy Lunin the opposite direction to send the home crowd into wildness.
Real had a big chance and subsequently their best opening to salvage something from the half through a one-one-one attempt by Luka Jovic, but Jan Oblak produced a solid save point-blank save.
The home team strengthened their stall just after halftime in the hope of maintaining their lead and had Antoine Griezmann come on ahead of Correa.
Los Blancos started the second half camping in Atleti’s half, whilst Carrasco fluffed two clear chances at the other end before Lunin pulled off a big close-range save to thwart Cunha.
Real responded in similar fashion in the final 20 minutes and saw a thumping strike from Federico Valverde from outside the area tipped over by Oblak.
It was a nervous closing few minutes for either side, none more after Carrasco leaned to the near post of the area and slammed Cunha’s low pass against the post.
Los Blancos didn’t stop unsettling Atleti inside the final exchanges, as another scorching strike from range by Valverde forced Oblak to another thumping save.
Real threw everything forward in pursuit of the equaliser, but Atleti held on tight to see out the win and the bragging rights.