Central defenders Jose Maria Gimenez and Diego Godin scored late to give Atletico the win, after the hosts had a penalty kick taken away and a goal disallowed by VAR.
The Serie A side bombarded the Atletico area with crosses but made little headway against a packed defence until Federico Bernardeschi switched to the left and floated a cross to the far post where Ronaldo outjumped Juanfran to head in.
Everybody thought Juventus were down and out.
The Spaniards had survived an early scare when Giorgio Chiellini's goal was disallowed after a VAR review.
But they seemed to forget about the powers of Cristiano.
Ronaldo was never going to miss, sending Oblak the wrong way to ensure Juve marched on at Atletico's expense, Diego Simeone's side going out of the competition after failing to record a shot on target in the second leg.
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We needed to move the ball faster, we needed more movements without the ball, more movements into space, behind the line.
Ronaldo did get the second goal three minutes after the break.
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However, Juventus also must defend with supreme commitment and focus, as one Atletico Madrid goal will require the Italian club to score at least four goals to advance.
Diego made the motion where he put his hands to his genitals on February 20 during Atletico's Champions League round-of-16 first leg.clash against Juventus when his team took the lead in the 78th minute 1-0, ultimately winning 2-0.
Juventus have progressed in a Champions League knockout tie having lost the first leg for the first time since 2005-06 v Werder Bremen.
Atletico Madrid is back in the round of 16 after failing to make it out of the group stage last season.