Ronaldo had taken his tally of European goals to 100 in the quarter-final win over Bayern Munich, which included a second-leg treble, and was once more the man for the big occasion to put the holders within touching distance of the final.
The Portugal forward headed Real in front on 10 minutes, although he appeared to have been offside in the initial build-up.
There was, though, no controversy about Ronaldo’s second goal with 17 minutes left as he lashed the ball in from the edge of the Atletico penalty area.
The Portugal star completed his hat-trick for the second successive Champions League fixture when he swept in Lucas Vazquez’s cut-back on 86 minutes.
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Atletico, beaten in last season’s final by Real, rarely threatened and now have it all to do at the Vicente Calderon next Wednesday night.
The two city rivals were meeting in Europe’s elite competition for a fourth successive year, with Real having also won the 2014 final.
Home fans at the Bernabeu unfurled a giant banner before kick-off which showed the venues of all of Los Blancos’ record 11 victories in the competition, which on this display could yet have Cardiff 2017 added to the list.
Atletico coach Diego Simeone had warned of a strong start from Real, and that is exactly what his team faced.
It was only a matter of time before Real took the lead. A cross from Sergio Ramos was nodded out only as far as Casemiro, who swung the ball in from the right towards the back post where Ronaldo powered a bullet header past Oblak. The goal stood even as Ronaldo appeared a yard offside when Ramos first played the ball in.
At the other end, Atletico finally came to life when Saul Niguez put Kevin Gameiro clear to run behind the Real defence, but goalkeeper Keylor Navas was out quickly to make a well-timed save.
Real were forced into a change at the start of the second half when Carvajal was replaced by Nacho, the defender having appeared to pick up a hamstring injury.
Simeone then looked to inject some fresh impetus into his side on 55 minutes when Gameiro and Saul were replaced by Fernando Torres and Nicolas Gaitan.
But on 73, their troubles doubled. Benzema held the ball up from Diego Godin at the edge of the Atletico penalty area before laying it off towards Ronaldo. Filipe Luis slipped as he tried to make a clearance, which saw Ronaldo latch onto the lose ball before firing past Oblak.
Atletico were cut open again with four minutes left when Vazquez charged to the goal-line and pulled the ball back to the penalty spot, where Casemiro stepped over it for Ronaldo to knock into the net and take the adulation of the Bernabeu once more.