The win came on the back of the F.A. Youth Cup victory over Burnley at Turf Moor and once again it was City's latest signing Asmat El Ouargui who scored the winning goal.
Saturday's game was scheduled to take place at Chelsea's new training ground at Cobham in Surrey but with work there not quite complete the game was played at their old training complex next to Heathrow Airport.
It was clear that the gale force cross-wind would play an important part in the game as both sides battled to overcome the difficult conditions.
Matthew Halliday heads clear
A Chelsea defender puts the squeeze on Robert Eagle
City looked to be mastering the conditions better than their hosts and went close with a free-kick from Robert Eagle, while Lewis made a comfortable save at the other end from a long range effort from Michele Gallaccio.
That was about it as far as the first-half was concerned, indeed there were not that many more opportunities after the break.
El Ouargui did well to create an opening for Michael Spillane but his shot across the goal was wide of the far post. Next it was the turn of Adam Gusterson, this time his looping effort looked a goal all the way until Makalambay pulled off a stunning save to turn the ball over the crossbar.
But City were not to be denied on the hour mark when Chris Martin did well to win the ball before picking out El Ouargui who had the time to picked his spot and blast the ball into the bottom left hand corner.
This appeared to spark Chelsea into life, although the City defence stood firm with fine displays by Andrew Cave-Brown and Gusterson.
Citys one moment of real concern came when Galliccaio sent a shot across the area that had Lewis scampering across his goaline.
City Line-Up: Lewis, Cave-Brown, Jarvis, Gusterson, Halliday, Howlett, Muddel (Willis 75 mins), Spillane (Smith 75 mins), El Oragio (Blackburn 65 mins), Martin. Eagle.
Sub Not Used: Herbert.
Top Canary: Adam Gusterson.
Seb Muddel and Robert Eagle congratulate Asmat El Ouargui on his goal
