Diego Costa broke the deadlock for the hosts in the 35th minute before David Faupala levelled two minutes later for City’s young side.
However, Brazil international Willian restored Chelsea’s lead just three minutes after the break before Gary Cahill added a third at Stamford Bridge.
Eden Hazard scored Chelsea’s fourth 23 minutes from time before Bertrand Traore sealed the west London side’s passage into the FA Cup quarter-finals with a late goal.
Former Liverpool midfielder Murphy praised Chelsea’s professional performance following a landslide win against the Citizens.
“You have to give Chelsea credit in the second half, it has been men against boys. They have been stronger, fitter, sharper and more creative with their passing,” Murphy told BBC Sport.
“This should be happening, it is no criticism of Manchester City. You can’t expect the youngsters to play with just two or three senior players around them.
“It is not the fact you are playing with youngsters, it is about playing against such quality. They have too much pride and passion to be undone by kids.”
Chelsea are 14 points behind fourth-placed City in the race to secure a spot in next season’s Champions League.
City make the trip to Ukraine on Wednesday night to face Dynamo Kyiv in the first leg of their Champions League last-16 tie.
Manuel Pellegrini’s side are in action against Liverpool in the League Cup final next Sunday.
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