Javier Hernandez got the winner in the 87th minute and judging by his celebrations after scoring, one realizes what a huge result this was for Real Madrid against a team that has troubled them in recent times.
This match was a repeat of last season's Champions League final which Real Madrid won but since then Atletico are unbeaten against their City rivals, winning four of the seven matches they've played so far this season.
And when you take into consideration that Real were without key players – striker Karim Benzema, winger Gareth Bale and midfielder Luka Modric – while full-back Marcelo also misses out through suspension. You realize just what they were up against minus these players.
By contrast, Atletico's only absentee was the suspended midfielder Mario Suarez.
The one thing that cost Atletico big time was not winning at last week's stalemate at the Estadio Vicente Calderón because in Champions League football you must win your games at home and if you don't that makes things so much more difficult.
Lets race it Real Madrid rarely lose at Estadio Santiago Bernabéu and that proved to be the case on Wednesday night.
During the first-half of Wednesday's game the home side were better in a scrappy half that was low on chances but Real should have taken the lead in the 43rd minute.
Mandzukic gifted possession to Carvajal on the edge of the penalty area. The ball was slipped through to Ronaldo, who only had Oblak to beat in a one-on-one, but the keeper was equal to the task and got down well to save and put the ball out for a corner. Ronaldo should have done better.
In the 75th minute things got a whole lot more difficult for Atletico when they had Turkish midfielder Arda Turan sent off for a second bookable offence for a slightly late challenge on Sergio Ramos as the pair contested a 50-50 ball, it was probably the right decision though.
In the 80th minute Hernandez missed a great chance to score when shaking off a challenge to burst into the Atletico penalty area to latch onto a beautifully weighted ball in between defenders from James Rodriguez. Oblak came out to narrow the angle and divert the low diagonal shot out for a corner. Great goalkeeping, but Hernadez should have given him no chance.
Then in the 87th minute Atletico's resistance was finally broken when Ronaldo surged into the area after a one-two with Rodriguez before sliding a pass to Hernandez who had a simple tap-in to score and win the match for his side.
The semi-finals of this year's Champions League sees great teams making the last four – Juventus, Real Madrid CF, FC Barcelona and FC Bayern München. It will be interesting to see who faces who when the draw is made on Friday.
Everyone has been talking up a storm about the form of Barcelona and Bayern. The German side overturned a 3-1 deficit against FC Porto with a 6-1 win to reach the semi-finals while Barcelona joined them after Neymar finished off Paris Saint-Germain for the Spanish giants to win 5-1 on aggregate.
BUT don't write Real or Juventus off as they are quality sides which leaves one with a mouth watering prospect of what is to come after Friday's semi-final draw.