Needing a convincing performance in Europe after a dreadful start in La Liga, Real twice came from a goal down in the Group D opener at the Bernabeu before Ronaldo struck a 90th-minute winner to send the home fans into raptures and silence the boisterous City supporters high up in the giant arena.
The fight the Real players showed to turn the game around was in stark contrast to the limp displays that led to shock domestic defeats at Getafe and Sevilla.
The victory against the English champions has transformed a club on the verge of crisis into a team full of belief they can secure the 10th European title that has eluded them since 2002.
Mourinho launched a series of stinging attack on his players after the La Liga setbacks but after wildly celebrating Ronaldo's goal the Portuguese told reporters Real could scarcely have played better.
"In Seville (on Saturday) we had players who did not win a ball in 90 minutes," he said. "Today was the opposite. The team was solid, compact, recovered balls and were committed to play aggressively.
"Real Madrid wants that historic tenth title and we will fight for it."
Concern in the Spanish capital about Real's early-season wobble was exacerbated by Ronaldo's revelation at the start of this month that he was "sad" for professional reasons.
The Portugal forward's bombshell prompted speculation he was seeking an improved contract and could even leave the club that made him the world's most expensive player when they bought him from Manchester United for 94 million euros three years ago.
Ronaldo's comments about his state of mind came after he refused to celebrate the two goals he netted in a 3-0 win at home to Granada.
Tuesday's winner, his 39th Champions League strike and his 151st goal in 151 appearances for Real, prompted a typically flamboyant reaction and he was mobbed by jubilant team mates.
He was asked whether it had been important for him to connect with the Real fans again.
"To be honest, I haven't thought about that at any time," he told reporters.
"What happened in the past doesn't matter. What matters is the present and the present is good. People are happy and pleased."
Asked how he was feeling, he replied: "That doesn't matter."
Real's next game is at city rivals Rayo Vallecano on Sunday, when they can begin the process of trying to close the eight-point gap to arch leaders Barcelona, who have won all four of their La Liga matches.
Tuesday's morale-boosting victory was the quick-fix they needed but there was a lingering sense on Wednesday that the club still has problems to deal with.
Mourinho left experienced Spain centre back Sergio Ramos, one of the club captains, on the bench on Tuesday, replacing him with French 19-year-old Raphael Varane.
Local media suggested all was not well between Ramos and his coach but Mourinho denied there was any rift.
"Ramos did not play because the coach thought it better that he did not play," Mourinho said.
"We're talking about a player in the starting eleven, a great, but I want to make clear that I have no problems with him whatsoever," he added.
"It's a purely football decision. I thought that Varane and Pepe were in better shape to play together today."
Ramos used his Twitter account to congratulate the team but did not address his omission from the team.
"I congratulate all my team mates for the great effort and the win in the Champions League," he wrote.
"Fantastic atmosphere in the Bernabeu. Go Madrid!"
- La Liga