A jubilant Mourinho made the most of the last-gasp victory, going onto the pitch at full-time and cupping his ear to jeers from the crowd, who had earlier cheered former Juventus player Paul Pogba on his return to Turin.
Juventus players Leonardo Bonucci and Paulo Dybala confronted Mourinho with United captain Ashley Young intervening as Mourinho was led off the pitch by a UEFA official.
"They insulted me for 90 minutes. I came here to do my job, nothing more," said former Inter Milan coach Mourinho. "I didn't offend anyone at the end, I just made a gesture that I wanted to hear them louder. I probably shouldn't have done it, with a cool head I wouldn't have."
Ronaldo's superb volley — his first European goal for Juventus — had put the Italian champions in control after 65 minutes, two weeks after Dybala scored in the only goal at Old Trafford.
Allegri hails 'leader' Ronaldo after victory
But substitute Juan Mata's free-kick on 86 minutes sparked a stunning revival that breathed new life into the visitors' Champions League campaign.
Juve were then left in shock as Ashley Young's free-kick from the left bounced in off a combination of Bonucci and Alex Sandro after a frantic scramble in front of goal.
It left Mourinho's side just two points behind leaders Juventus with two matches to play in Group H.
"It's a fantastic victory for us, a victory that is not just about the points we lost at home but the feeling of how well we played," said Mourinho. "And I think even if this game hadn't ended with victory I would have the same feeling that the team played really, really well from the first minute against a super team."
City shrug off FFP furore to hit six
Allegations of financial impropriety off the field couldn't derail Manchester City moving to the brink of the Champions League last 16 as Gabriel Jesus scored a hat-trick in a 6-0 thrashing of Shakhtar Donetsk on Wednesday.
A series of allegations published by German magazine Der Spiegel in recent days claim City attempted to bypass UEFA's Financial Fair Play (FFP) regulations, but the English champions showed no signs of distraction as they swatted the Ukrainian aside and took control of Group F.
Benzema brace helps Real thump Plzen
Karim Benzema's first-half brace propelled Real Madrid to a 5-0 thrashing of Viktoria Plzen in the Champions League on Wednesday, putting the holders one win from the last 16 after a third straight victory under Santiago Solari.
Former Real midfielder Solari took over from the sacked Julen Lopetegui as interim coach on October 29, and has now seen his side score 11 times without reply following wins over Melilla and Real Valladolid.
Meanhwhile, Hoffenheim revived their hopes of reaching the Champions League last 16 as Pavel Kaderabek scored an injury-time equaliser to cap a dramatic comeback with 10 men and snatch a 2-2 draw at Lyon.
First-half strikes from Nabil Fekir and Tanguy Ndombele put Lyon in control at the Groupama Stadium, and Kasim Nuhu's sending off shortly after the restart left Hoffenheim with a mountain to climb.
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