Emanuelson was on hand to tap home the rebound from close range after 67 minutes when a shot from Stephan El Shaarawy was saved by Petr Cech.
Chelsea's best chance came early in the game but when Lampard's delivery was headed back across goal by Branislav Ivanovic the loose ball was fired over the bar by John Terry who slipped just as he was about to shoot.
Lampard nearly set up Emanuelson for the opener early in the second half when he gave the ball away to the Dutchman but after beating Terry he shot at Cech.
Emanuelson made no mistake with 13 minutes to go when he forced the ball home following Cech's save from El Shaarawy.
The Chelsea goalkeeper then did well to save at the feet of Mattia Valoti as Milan tried to extend their lead late in the game.
Despite the defeat at least manager Roberto Di Matteo got to see summer signings Eden Hazard and Marko Marin in action for the Blues on the latest leg of their tour of the United States.