In-form striker Tammy Abraham gave the visitors the lead after just seven minutes at Academy Stadium, but City were quickly back on level terms after Isaac Buckley-Ricketts beat goalkeeper Bradley Collins with a low effort.
Abraham then took his tally for the season to 36 goals by netting his second of the evening from close range and the equally prolific Dominic Solanke, who now has 10 strikes to his name in this competition alone, increased Chelsea's advantage late on after City had pressed forward in vain.
While it is important to note that the away goals rule does not apply to the Youth Cup, you sense that it will be difficult for Jason Wilcox's side to overturn such a deficit when the teams meet again at Stamford Bridge on 27 April.
If indeed Chelsea do go on to win the trophy, then it will be just the latest success of an impressive season for the club's youngsters.
Although the U18s lie fifth in Group One during the final stages of the Premier League season, the U19s proved their quality on the continental stage earlier this month by beating Shakhtar Donetsk 3-2 to claim the UEFA Youth League title.
Chelsea and first-team manager Jose Mourinho are often criticised for the lack of an obvious pathway for younger players through to the senior squad.
However, with the likes of Abraham, Solanke and Isaiah Brown showing such potential, supporters will hope that a number of the current crop will be able to establish themselves in West London rather than follow countless others into a rut of endless loan spells with seemingly little prospect of reaching the required standard.