A deflected free-kick in the first half, a penalty after 71 minutes and a fine counter-attacking finish were enough to give the visitors the bragging rights and make Ronaldo the top scorer in the history of the derby.
Atletico started with Antoine Griezmann in attack, despite concerns over a foot injury, but the France star was barely involved as Diego Simeone’s side slumped to a damaging defeat in the final LaLiga meeting with their city rivals at the Calderon.
Madrid lined up in a 4-4-2, with Ronaldo playing just ahead of Isco and Gareth Bale and Lucas Vazquez deployed out wide, and their shape appeared to have Atleti flummoxed as they struggled to keep possession or make any inroads on the break in the first half.
Ronaldo’s free-kick, which deflected off Stefan Savic, deservedly put the visitors ahead and they withstood a short spell of sustained pressure early in the second half before Ronaldo struck from the spot.
A fine counter-attack involving Bale gave the Portugal captain his 18th derby goal before he was replaced to a standing ovation from the visiting faithful, who celebrated their side moving four points clear of Barcelona at the top of the table, and nine ahead of Atletico.
Ronaldo brought the first save of the match from Jan Oblak, his header from Marcelo’s deep crossing forcing the Slovenia international to claw the ball superbly off the line low to his left.
Madrid were pressing well from the front and Luka Modric brought another good low stop from Oblak after first Ronaldo and then Bale had won back possession close to the Atletico area.
With 23 minutes played, Madrid found the breakthrough. Ronaldo’s 30-yard free-kick from a central position glanced off Savic in the Atletico wall and bounced past the wrong-footed Oblak and into the net.
Madrid looked comfortable in their 4-4-2 set-up, while Atletico for once seemed unsettled by a tactical switch-up from their opponents, and Ronaldo missed a good chance to double the visitors’ lead when he spun into space after Isco’s pass only to shoot straight at Oblak.
The home side looked invigorated after the interval, however. Yannick Ferreira Carrasco’s shot had Keylor Navas scrambling before Griezmann twice had the Madrid keeper worried, first drilling across goal and out before testing his handling with a dipping strike from distance.
Simeone introduced Angel Correa and Kevin Gameiro from the bench to create a front three alongside Griezmann, but it was Madrid who came closest to a second, with Isco’s low shot from the edge of the area pushed around the right-hand post by Oblak.
And a minute later, Atleti offered the visitors the chance for the killing blow. Savic slipped while trying to clear the ball and proceeded to trip Ronaldo as he closed him down, allowing the Portugal skipper to step up and sweep home from the penalty spot into Oblak’s bottom-right corner.
Atleti pushed forward in search of a lifeline and, six minutes later, they were undone by a brilliant counter-attack. Bale surged into the Atletico box and cut the ball back across goal for Ronaldo, who could not miss from three yards out at the far post.
Zinedine Zidane brought off his star forward seven minutes to play, with the points secured and the title race now firmly in their hands.