Charlie Colkett delivered the killer blow four minutes from time as the EDS wrapped up their Barclays U21 Premier League campaign at the Etihad Stadium.
Simon Davies made two changes to the side that beat Liverpool 2-0 on Friday with Angelino and Aleix Garcia replacing Cameron Humphreys and Manu Garcia.
The opening to the game was dominated by the young Blues, who created two chances in the opening ten minutes.
First, George Glendon latched onto a Brandon Barker through ball before seeing his shot palmed away by Bradley Collins before the Chelsea shot stopper was in action again to deny Sinan Bytyqi.
The away side had their moments and created two chances of their own midway through the first half, but Angus Gunn was in fine form to keep them at bay.
The 20-year showed great reactions to prevent Ruben Sammut’s effort hitting the back of the net and then pulled off another good save seven minutes later to tip Mukhtar Ali’s shot around the post.
City pushed bodies forward in an attempt to open the scoring late in the first half and came close in the 37th minute.
Isaac Buckley played a through ball that split the Chelsea defence and released Barker, who steadied himself before firing narrowly past the outside of the post.
The second half was a much quieter affair with both sides cancelling each other out in midfield.
The young Blues were solid in possession and created a chance 13 minutes after the restart. Bersant Celina squared the ball to Bytyqi, who took a touch to set himself and then shot inches wide of Collin’s goal.
Chances were few and far between in the second period with the impressive Bytyqi having City’s next chance in the final ten minutes.
The Austrian midfielder burst into the box from the left hand side and got a shot away, only to see a strong hand from Collins push his shot out for a corner.
Davies’ side continued to soak up the pressure from Chelsea before the away side stole the three points in the 86th minute.
Tosin Adarabioyo put in a great challenge to prevent Ike Ugbo getting a clear shot on goal and the rebound fell to Colkett, who slotted home from eight yards to snatch the win.