Carlo Ancelotti's side brought a 3-2 advantage into the return fixture, and the reigning European champions had no trouble from the Citizens on the night, with Mbappe hitting a treble to secure a 6-3 aggregate success.
Mbappe made the breakthrough just four minutes into the contest before adding another in the 33rd minute; the Frenchman then completed his hat trick just past the hour to cap a stunning performance in the Spanish capital.
Man City did have a late consolation at Bernabeu, though, courtesy of a close-range finish from Nico Gonzalez.
Real Madrid will take on either Atletico Madrid or Bayer Leverkusen in the next round of the competition, while Man City's focus is now on the Premier League and FA Cup, with the latter representing their best chance of silverware this term.
SPORTS MOLE'S VERDICT
This was an incredibly tough night for Man City and their head coach Pep Guardiola.
There was not a single moment in the match when the Citizens looked capable of picking up a good result, with Real Madrid the dominant outfit from the first whistle to almost the last, and Ancelotti's side sent out a statement here.
Real Madrid have been far from perfect this season, and they are no longer top of the La Liga table, but the capital giants are serious challengers to win Spain's top flight and the Champions League once again, while the team are present in the semi-finals of the Copa del Rey.
Any side with Mbappe, Vinicius Junior, Rodrygo and Jude Bellingham as a front four has a serious chance, and it could have been more comprehensive on the night such was Real Madrid's dominance.
Without Erling Haaland, Man City had no real goal threat, and without Kevin De Bruyne, there was no real creation.
It was a worrying night for the Premier League champions, who are having a tough campaign, and being eliminated at this stage of the Champions League is a serious disappointment considering their recent record in Europe.
REAL MADRID VS. MAN CITY HIGHLIGHTS
Kylian Mbappe goal vs. Man City (4th min, Real Madrid 1-0 Man City)
Real Madrid make the breakthrough in the fourth minute of the contest, and it is a wonderful finish from Mbappe, who lifts a long Raul Asencio pass over Man City goalkeeper Ederson - incredibly poor defending from the Premier League champions there, with Ruben Dias losing his footing moments before Mbappe produced the lobbed finish.
Kylian Mbappe goal vs. Man City (33rd min, Real Madrid 2-0 Man City)
Real Madrid have their second of the match, and it is a brace for Mbappe, who sits Josko Gvardiol down inside the Man City penalty box before firing the ball into the bottom corner - devastating from Los Blancos, who have been exceptional thus far tonight.
Kylian Mbappe goal vs. Man City (61st min, Real Madrid 3-0 Man City)
There is the hat trick! Mbappe scores his third, as he cuts onto his left foot before firing the ball into the bottom corner of the net - that is his 28th goal of the season for Real Madrid, who are heading for the next round of the competition.
92nd min: Real Madrid 3-1 Man City (Nico Gonzalez)
Man City have a late consolation at Bernabeu, as Gonzalez taps home from close range after Omar Marmoush's free kick smashes against the Real Madrid crossbar; the goal is eventually given following a lengthy VAR check.
MAN OF THE MATCH - KYLIAN MBAPPE
Federico Valverde is incredibly unfortunate to miss out on this award considering his display, with the Uruguay international an inspirational figure for the Spanish giants from an unfamiliar right-back position.
However, the man-of-the-match award simply has to be given to hat-trick hero Mbappe, who was in sensational form against Man City; the Citizens just could not live with the 26-year-old, who is now on 28 goals for the campaign.
REAL MADRID VS. MAN CITY MATCH STATS
Possession: Real Madrid 48%-52% Man City
Shots: Real Madrid 15-12 Man City
Shots on target: Real Madrid 8-4 Man City
Corners: Real Madrid 7-5 Man City
Fouls: Real Madrid 9-9 Man City
BEST STATS
WHAT NEXT?
Real Madrid will take on either Atletico Madrid or Bayer Leverkusen in the next round of the Champions League, while Man City's journey in the 2024-25 competition is over, and their exit at the playoff stage is a huge surprise.
Man City's attention will now switch back to the Premier League, preparing to welcome Liverpool to Anfield on Sunday for a huge fixture, while Real Madrid's La Liga title defence will continue at home to Girona on the same afternoon.
Written by
Matt Law