On 76 minutes, Ronaldo pulled his side back into the contest when heading home Casemiro's lovely ball from the right before a calamitous own-goal, nearly immediately, from Sergio Ramos saw Bayern again edge ahead on the night.
The defending champions led 2-1 from the away first leg, but lost 1-2 for a 3-3 aggregate at full time in the home second leg before Ronaldo's intervention.
Real Madrid hosted Bayern Munich at the Bernabeu tonight, and came into the game holding a 2-1 advantage from the first leg. "It hurts to go out in extra time, but we were a man down for over an hour across the tie".
However that goal was too criticised by viewers for being offside.
Ronaldo resting, Isco's 2 goals keeps Madrid on title track
Madrid travel north on the back of their 2-1 win away over Bayern Munich in the Champions League and with their morale sky high. I think we deserved the victory because we had many chances to score more goals. "We need everyone and everyone responds".
"The referee's task is quite hard, whether it's for or against us I won't get into it", said Madrid coach Zinedine Zidane.
"Cristiano answers on the pitch, and he scored three goals, five in two games, what else can I say", Zidane added.
For the fourth time in a row, Bayern Munich were knocked out of the Champions League by a Spanish side.
"We're very angry, a game with that much intensity can't be decided by the referee". "I think the team deserved to go through".
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Cameron Carter-Vickers is also a doubt for the game while Harry Winks and Erik Lamela will not feature again this season. Bournemouth midfielder Dan Gosling remains doubtful after suffering a setback to his recovery from a knee problem.
"Madrid were better, it's not easy to score six goals against Bayern".
Ronaldo appeared to respond by gesturing for the fans to be quiet as he celebrated his goals, but Zidane insists the Portuguese will not face retribution from the club's supporters when Real face Barcelona in this Sunday's El Clasico, live on Sky Sports 1HD.
Two minutes later, though, Ramos found his own net when his deflection sent the ball trickling across the goal line.
You can't decide a Champions League semi-final spot like this.
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Joseph Jakubowski's stepfather, Don McLean, said he fears his stepson is a risky man and may want a showdown with police. It says Jakubowski is willing to die if it happens through the intervention of the president, and on live television.
Isco hit back at criticism of Real Madrid's victory over Bayern Munich as the Germans "were awarded a penalty that wasn't one".