Photo: AFP
The Portugal star, who racked up a century of goals in Europe in the first leg, headed in his first of the game on 76 minutes before firing Real back ahead in the tie on 105 minutes.
Ronaldo struck his third goal five minutes later to all but secure Real's place in the semi-finals.
Honour to become first to score 100 goals in Europe: Ronaldo
He has now scored 85 goals in 85 appearances in the Champions League for Madrid.
He also netted 15 in the competition and one in a qualifier for Manchester United prior to moving to the Spanish capital in 2009.
Tuesday's treble extended Ronaldo's lead over Barcelona rival Lionel Messi as the top scorer in Champions League history.
Messi has 94, 11 of which have come in this season as the competition's top scorer.
However, the Argentine is unlikely to have many more opportunities to add to that tally this season after Barcelona were thrashed 3-0 by Juventus in the first leg of their quarter-final tie.
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