He slammed home Real's second goal with 17 minutes remaining and then added a third late on to continue Real's dominance over their neighbours in Europe's premier club competition.
They won both the 2014 and 2016 Champions League finals against Atletico, and eliminated them at the quarter-final stage during the 2014-15 campaign.
And, as they take a 3-0 lead to the Vicente Calderon next Wednesday, Real are odds-on favourites to make the June 3 final at the Millennium Stadium in Cardiff.
Ronaldo, who scored his 42nd hat-trick for the club and took his season's goal tally to 35, added: 'The team has been tremendous.
'It was my turn to score the goals, but the team was phenomenal. It was a perfect match, we have a good advantage, but it's not over.
'Atletico are very good, but we must be careful on Wednesday.'