About 4,500 Bayern fans travelled to watch the Germans bow out 6-3 on aggregate, after going down on the night 4-2 in extra time in the quarter-final second leg.
However, the victory did not come without controversy as Ronaldo was shown to be in an offside position when he scored his second goal while Arturo Vidal was harshly sent off for the visitors. "It makes you very angry".
Bayern Munich have complained to UEFA after clashes between police and their supporters during the Champions League defeat to Real Madrid at the Bernabeu. "When Madrid got scared, the referee began his show", Vidal said.
"You are talking about one of the greatest players ever to play this game".
Zinedine Zidane's team are bidding to become the first side to successfully defend the Champions League.
VARs - which rule on key incidents concerning goals, red cards, mistaken identities and penalties - could be used in English football as early as August, with the EFL Cup first round touted as a possible initial testing bed for the technology.
Vidal said: "It is very tough when they steal a game from you like that - two goals offside and me wrongly sent off". A game of such high intensity can't be decided by the referee. He came into the series against Bayern in a scoring drought of almost seven months in the European tournament, and had scored only once in his last five Madrid games in all competitions. But Atletico, who have reached two finals in the last three seasons, remained tenacious on defence and managed to see out the match.
"I don't think Real Madrid have any influence on referees. It's time to introduce videos for the referees". "Although I don't always score, I always work hard and try to help Real Madrid".
Ronaldo levelled the scores after Robert Lewandowksi's opener as he headed home Casemiro's cross.
Lahm and Alonso both retire from all football at the end of the season. "More than the second yellow [for Vidal] or the offside goals, the six goals we scored over the two games means we deserved to go through in the tie".
Lewandowski, who captains the Polish national squad, stormed into the referee's dressing room after the match accompanied by Spain's Thiago Alcantara and Vidal to express their opinion, Spanish media wrote.
The trio are said to have launched stinging insults at the Hungarian official and laid the blame for the result squarely at his feet.