Atletico had held a two-goal advantage heading into the second leg of the last-16 tie in Turin, but Ronaldo wiped out that lead within 49 minutes.
Ronaldo completed his treble with a late penalty, and the result keeps Juve on course for a Serie A and European double in what could reportedly be Massimiliano Allegri's last season in charge of the club.
Juventus went into the contest knowing that an early strike would benefit their chances of progression, and the home side were left feeling aggrieved when they harshly had an early strike chalked off by a combination of the referee and VAR.
Giorgio Chiellini fired home from close range after a goalmouth scramble from a corner, but both the referee and VAR controversially ruled that Ronaldo had kicked the ball out of the hands of goalkeeper Jan Oblak.
The incident had the potential to hinder Juventus, but to their credit Allegri's side continued about their business as they went in search of a much-needed goal.
Federico Bernardeschi moved over to the left-hand side of the penalty area to deliver a cross for Ronaldo, who powered a header inside the near post from close range after getting the better of Juanfran.
Bernardeschi went close with a free kick soon afterwards as Oblak watched the Italian's set piece go marginally over the bar, while Ronaldo and Chiellini also failed to add a second for their side with headers just before half time.
However, Atletico wasted a glorious opportunity to leave Juventus requiring three second-half goals as Alvaro Morata sent a header over the crossbar from no more than 10 yards out.
Atletico were made to pay soon after the restart as Juventus and Ronaldo netted their second of the evening, with the forward's towering header going inches over the line despite the best efforts of Oblak.
Juventus remained in the ascendancy without forcing Oblak into any further action between the sticks, while Atletico were being restricted to shots from distance with Angel Correa firing harmlessly wide.
Both managers opted to make a number of alterations throughout the second half, but there was an awareness that a third goal of the contest would be decisive.
Juventus should have moved ahead on aggregate with eight minutes remaining through substitute Moise Kean, but the youngster dragged a volley wide of the far post from 10 yards out after being played through on goal.
However, Ronaldo spared his teammate's blushes shortly afterwards. Juventus were awarded a penalty when Bernardeschi was pushed by Correa inside the area, and the 34-year-old stepped up to dispatch the penalty into the bottom corner.
Juventus still had to see out the closing stages with an Atletico goal being enough to eliminate the 2015 and 2017 runners-up, but the visitors barely threatened in the second half as Diego Simeone's side became the latest high-profile club to bow out of this year's competition.
JUVENTUS (4-3-3): Szczesny; Cancelo, Bonucci, Chiellini, Spinazzola (Dybala 67'); Can, Pjanic, Matuidi; Bernardeschi, Mandzukic (Kean 80'), Ronaldo
ATLETICO MADRID (4-3-3): Oblak; Arias (Vitolo 77'), Gimenez, Godin, Juanfran; Koke, Saul, Rodri; Lemar (Correa 57'), Morata, Griezmannbody check tags ::