Bayern Munich players were very happy after the game at Santiago Bernabéu.
Following the clashes between Leicester City supporters and officers that preceded last week's quarter-final first leg between Atletico Madrid and the Premier League champions, authorities in the Spanish capital pledged to reinforce its police presence for Bayern's visit.
Questions remain over whether two of his goals should have stood - and that's an understatement, because they were both offside - but you can't take anything away from him.
Ronaldo has now scored 395 times in 386 outings for Madrid and has 518 goals in 711 club appearances in total.
Neuer, outstanding in both legs against Real, was injured in extra-time and will miss the final stretch of the season with Bayern leading by eight points in the Bundesliga with five matches remaining.More news: North Korea video portrays US destroyed in missile barrage
He followed up the snapshots of the decisions with another Instagram post in his story that said: "One year of hard work, thank you referee, bravo".
Just what Ronaldo deserved - his goals may have been offside, but he was once again the hero.
Ronaldo's second on the night and first in extra time looked the more clear cut decision, while his treble-completing strike seems a little tougher to call.
"Sometimes when he doesn't score we wonder what's happening to him. He made a lot of mistakes and he left us out of the Champions League".
Bayern Munich coach Carlo Ancelotti said Uefa must swiftly introduce video technology.More news: Dortmund are no dreamers but still in with a chance - CEO
Victory also secured history on a collective level for Madrid as they reached the semifinals for a record seventh straight year. "But now I'm feeling good and the team has been playing really well, that's what's important".
His Real Madrid counterpart Zinedine Zidane did not want to discuss the refereeing but he claimed Bayern's second goal could have also been ruled offside.
"Maybe they will not whistle him any more", said Zidane in defense of his star man.
"The fans will always appreciate Cristiano for all he has done here".
"We were in great shape mentally after we went 2-1 up and still had 11 players on the pitch".More news: Fox News Channel dismisses O'Reilly, its biggest star
"He scored three goals and the fans will be grateful for what Cristiano has done".
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