Twice City led at the Etihad as Erling Haaland finally came to the party against the Spanish giants with his first two goals in five games against Madrid.
But the Norwegian’s goals cannot paper over the glaring cracks for City this season.
Madrid had been wasteful for 85 minutes and would have headed home cursing their finishing but for a late flourish.
Brahim Diaz netted against this former club just seconds after coming off the bench before Jude Bellingham, on his return to England, tapped home the winner in stoppage time after another City defensive calamity.
City have now conceded eight goals in the final 15 minutes of their last five Champions League games.
Late goals have also been a problem for Guardiola in the Premier League, where City sit a distant 15 points behind leaders Liverpool.
Despite winning just three of their eight previous Champions League games this season, City sneaked into the play-off round on the final night of the league phase.
However, they paid the price for finishing 22nd in the 36-team table by being paired with the 15-time European champions.
The clubs are facing off for the fourth consecutive season in the Champions League.
Madrid came out on top in two of the previous three ties, but on each occasion their trip to the Etihad was a chastening one.
In 2022 and 2023, Carlo Ancelotti’s men shipped four goals, while last year they clung on bravely for a 1-1 draw before progressing on penalties.
This time it was a different story, long before the late twist in the tale.
“It was a weird one. We played some of our best football of the season and ended up behind,” said Bellingham.
Ageing City
Madrid could have struck three times inside the first 15 minutes through Vinicius Junior, Kylian Mbappe and Ferland Mendy.
A series of more chances came and went before Mbappe cancelled out Haaland’s opener with a fortunate mishit.
Haaland restored City’s lead from the penalty spot 10 minutes from time.