Graham Potter's side took control at a packed San Siro against a Milan team who had to play most of the match with 10 men after Fikayo Tomori was controversially handed an early straight red card.
The decision to send off Blues man Tomori for fouling Mason Mount in the area in the 18th minute turned the match on its head as Milan had matched Chelsea in the opening stages.
Milan coach Stefano Pioli kept a calm demeanour after a painful defeat but later told reporters: "I definitely don't think the referee has had one of his better evenings."
It's been a quick turnaround for Chelsea, who were bottom of the group going into the first match with Milan at Stamford Bridge last week and now lead the way after their fourth win on the bounce in all competitions.
Two straight defeats to Chelsea leave Milan third but they still have a fighting chance of making the knockout stages for the first time since the 2013-14 season.
Pioli's side are ony two points away from the qualification places and a trip to Dinamo Zagreb and the visit of Salzburg will decide their fate in the competition.
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