Ronaldo bagged his 121st goal of all-time in the competition, lashing home an incredible volley after a long ball over the top from Leonardo Bonucci, but Juan Mata's 86th minute free kick levelled and Alex Sandro's own goal in the final minute sealed a much-needed win.
Ronaldo had the first chance inside five minutes as he managed to stay onside, but could only clatter his shot against Victor Lindelof.
United looked confident in possession in the opening exchanges but it was Juventus who had another chance shortly after as Rodrigo Bentancur's shot from outside the box was deflected behind for a corner.
Nemanja Matic went into the book inside 12 minutes for a shocking tackle on Paulo Dybala but the Serbian was on hand to block from Juve's No. 10 as he tried to wiggle his way into the box.
Juventus controlled things but a clipped ball to Alexis Sanchez almost opened the door at the other end, only for it to be just out of the Chilean's reach.
Sanchez then should have done a lot better from a freekick, only managing to hit Ronaldo in the wall, before a quick counter attack saw Sami Khedira blast the ball into David De Gea's hands from 25 yards.
De Gea was called into action again as Juan Cuadrado's cross deflected off Matic and forced him into a fine save. And the United keeper was then saved by the post as Ronaldo's low cross found Khedira unmarked in the middle of the penalty box, but the German's shot hit the woodwork.
Paul Pogba had a long shot which was comfortably gathered by Wojciech Szczesny and United held firm under pressure before the half-time whistle sounded.
Immediately after the break, United had a chance as Anthony Martial sent an effort just wide from the edge of the box.
And, minutes later, Dybala went even closer at the other end as he picked up the ball after some neat interplay to curl an effort off the crossbar with De Gea well beaten.
Juve needed something special to break the United resistance and they got it when Bonucci's hopeful long ball from his own half dropped into the path of Ronaldo, who lashed it home on 65 minutes.
With their confidence flowing, the home side almost bagged a second, but De Gea palmed away Miralem Pjanic's low shot. Moments later, Pjanic had another chance but curled his effort wide of the post.
And it should have been 2-0 when Ronaldo squared for Cuadrado, only for the Colombian to inexplicably spoon his shot over the bar from close range.
Marcus Rashford came on to try and spark United into life, and almost equalised with a sharp turn and shot that skimmed wide with just over 10 minutes left.
United continued to press as Szczesny was forced into his first real save of the game from Martial. And moments later, Mata's perfect free kick from just outside the box levelled things.
Then United were ahead. A ball into the box was headed on by Marouane Fellaini and Sandro got the final touch as the ball was bundled over the line. Szczesny then had to deflect a Rashford shot over the bar when the United striker was free on goal as United sealed a remarkable comeback.
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