Bayern, who trailed 2-1 from the home leg against Madrid, made a fight of it on Tuesday night as they levelled the tie at 3-3 after 90 minutes to force extra-time.
It gave Madrid the upper hand going into the added 30 minutes and they took advantage when Ronaldo scored the crucial second from Ramos's cross, despite being in an offside position.
Ronaldo's first 15 Champions League goals came for United - including a towering header in the victorious 2008 final against Chelsea in Moscow - before he joined Madrid in 2009 for what was then a world-record fee of €94million.
"In the first leg, Bayern were wrongly awarded a penalty".More news: Marlins' Chen, Ziegler no-hitting Mariners through 8 innings
But Arturo Vidal was sent off with a controversial second booking, and they eventually lost 4-2 - 6-3 on aggregate - to miss out on the biggest club prize in Europe.
Manager Zinedine Zidane lavished praise on the team's all-time top scorer but reminded Ronaldo that Real players had to get used to the relentless pressure from supporters of the 11-time European champions.
With the German side needing to score twice, Ronaldo finished his hat-trick and Asensio also scored as Madrid twice caught Bayern on the break.
The Bayern shot-stopper and Germany captain suffered the injury while trying unsuccessfully to stop Cristiano Ronaldo netting his third goal in the 109th minute at the Bernabeu as defending holders Real won 4-2 after extra-time on Tuesday.More news: UK Foreign Secretary Cancels Moscow Visit
Bayern coach Carlo Ancelotti agreed with Vidal and said in his media conference that the referees needed video help.
"In a quarter-final, you have to put a better referee, or it is the moment to introduce video refereeing, which is what UEFA are trying, because there are too many errors", said the Italian. "There are decisions that have penalised us a lot".
"Real didn't know what to do, we were always controlling the game and in the end everyone is angry".
"Bayern feel the behaviour of the Spanish police is utterly out of place and excessive, and have lodged a complaint with UEFA about the actions of the Spanish police". Thomas Mueller said he found it hard to blame a referee for a defeat "but today there's no way around it". Robert Lewandowski was adjudged offside when clean through on goal.More news: Xiaomi Launches Flagship Mi 6 Smartphone With 6GB RAM In China
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