A Juan Mata free kick on 86 minutes followed by an Alex Sandro own goal as injury time approached gave Jose Mourinho's side a win that looked unlikely for most of the match.
Juventus had hit the woodwork twice before Ronaldo opened the scoring with a spectacular volley in the 64th minute.
And although Juve came close to extending their lead through Miralem Pjanic and Juan Cuadrado, they somehow contrived to throw away the lead in the closing stages.
That was of little concern to Manchester United who move back into second place in Group H above Valencia who defeated Young Boys 3-1 earlier Wednesday.
United boss Mourinho stormed onto the pitch and cupped his ears on the full time whistle to the chagrin of the of the home crowd who jeered loudly.
Afterwards the Portuguese, who had to be escorted off the pitch, said he should not have reacted.
"I didn't offend anyone at the end, I just made a gesture that I wanted to hear them louder," he told reporters.
"I probably shouldn't have done it, and with a cool head I wouldn't have done it, but with my family insulted, including my Inter family, I reacted like this."
Mata told UK broadcaster BT Sport that it was a "very good night for us."
"To get the three points against Juventus in Italy is amazing," he added.
Juve's fortress breached
Juventus came into the game on the back of a remarkable run of games that had seen them play 14, win 13 and draw one this season.
They also hadn't lost a Champions League game at home since 2009 when they were beaten by Bayern Munich.
It looked like another victory was on the cards after Ronaldo opened the scoring.
The Portuguese striker, the Champions League record goalscorer, smashed a spectacular volley past United keeper David de Gea after running onto Leonardo Bonucci's lofted pass.
Ronaldo played for United between 2003 and 2009 winning three Premier League titles as well as the 2008-09 Champions League.
His goal Wednesday also came at the same end of the ground where he scored a spectacular bicycle kick
for Real Madrid, another of his former clubs, earlier this year.