Luka Modric's miss handed Pep Guardiola's side the early advantage, before both Silva and Mateo Kovacic missed from the spot, as Real Madrid dispatched their next four penalties to progress.
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It was a bitter pill to swallow for the reigning UEFA Champions League holders, who dominated for most of the proceedings on home soil.
Kevin De Bruyne's effort cancelled out Rodrygo's opener, in what turned out to be a relatively one-sided game overall.
Former City star Joleon Lescott highlighted how Silva's mind must have been racing due to the long pause before his penalty kick.
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"That would have just took him out of sync and out of his rhythm," he began speaking via TNT Sports.
"You can practice the routine, the technique, the walk up potentially, this is something you don't prepare for, the ball being in the crowd."
Real Madrid celebrate their penalty-shootout success against Manchester City. (Image credit: Getty Images)
"That is a long time. It may not seem that long but it's a very long time when you are waiting there and you are thinking, now do I change position? Now do I change where I go? And all of a sudden, it's a soft penalty," added Lescott.
Rio Ferdinand shared further light on the situation, adding how Silva's wait for the penalty almost totalled a minute.
"Forty seconds by the way Joleon. It's a shame though as well, because it is the home fans that are delaying that penalty kick which is a shame."
Bio: Matthew is a freelance journalist and has currently racked up bylines for Manchester United, Manchester Evening News, GOAL and SPORTbible to name a few. A long-term sufferer of Scunthorpe United, he currently resides in the north-west after escaping the smog of North Lincolnshire.
