Real Madrid dominated the early proceedings at the Bernabeu, outshooting the visitors 11-0 in the opening half-hour as Ronaldo headed home in the 10th minute, before he lashed home a second midway through the second half and completed his treble five minutes from time.
The hosts first scoring opportunity came in the seventh minute as Dani Carvajal danced into the box and saw his shot saved back into the middle by Jan Oblak, though Karim Benzema's follow-up shot was blocked.
But Madrid were in front three minutes later as Casemiro chopped a cross into the ground, and as it bounced high into the box Ronaldo rose highest to head it into the net.
It was very nearly 2-0 a minute later, but Oblak made a superb diving save to deny Raphael Varane's header following a corner.
One of Atletico's few chances to equalise came soon after as Kevin Gameiro was played in on goal and tried to take a touch around Keylor Navas, but the Madrid goalkeeper got a hand to the ball to cut out the play.
Madrid continued to control matter as Luka Modric fired inches wide on 24 minutes and Benzema's audacious overhead attempt also fell on the wrong side of the post.
The game settled down significantly after that point, with scoring chances at a premium, while Nacho came on for Real Madrid at half-time after Carvajal appeared to pick up an injury.
The second half started equally slow, and Real Madrid didn't take a shot until Ronaldo doubled their lead in the 73rd minute.
Benzema shrugged off a challenge from Atletico's Diego Godin and the ball came to Ronaldo, who was tackled by Felipe Luis, only for the ball to come back off the Portugal star's body, and he slammed home his second goal of the night on the half-volley.
Atletico still failed to register a shot on target, and Ronaldo made it three following a counter-attack. Lucas Vazquez did well to take the ball to the endline and cut it back to find Ronaldo, who had time to take a touch and send Oblak the wrong way.