Former Real Madrid striker headed Federico Bernardeschi’s cross past Jan Oblak midway through the first half, scored yet another header three minutes after the interval from a Joao Cancelo delivery, and then netted from penalty spot four minutes from time for his eighth Champions League hat-trick.
Ronaldo has now scored 25 goals against Atletico in 32 appearances.
Bosnian midfielder Miralem Pjanic played the full 90 minutes in what turned out to be one of the greatest Juve’s comebacks in history. They had been eliminated in all five previous European ties in which they lost the first leg 2-0 away from home.
This was also the first time Juventus have overturned a first-leg defeat to go through since the 2005/06 round of 16 against Werder Bremen.
Elsewhere on Tuesday night, Manchester City registered their biggest ever European victory, and equaled biggest single-leg win in Champions League with 7-0 thrashing of Schalke.
Sergio Aguero scored two goals, Leroy Sane, Raheem Sterling, Bernardo Silva, Gabriel Jesus and Phil Foden added one each for Pep Guardiola’s side.