Emanuelson was on hand to tap home the rebound from close range after 67 minutes, despite Petr Cech saving the initial Stephan El Shaarawy shot.
Chelsea’s best chance came early in the game, but when Lampard’s cross was headed back across goal by Branislav Ivanovic the loose ball was fired over the bar by John Terry.
Lampard then nearly gifted Emanuelson the opener for the Serie A side when he gave the ball away to the Dutchman, but after gliding past Terry he could only fire straight at Cech.
However, Emanuelson made no mistake midway through the second half when he forced the ball home following Cech’s save from El Shaarawy.
The Chelsea goalkeeper then did well once again to save at the feet of Mattia Valoti as Milan tried to extend their lead late in the game.
Although there was the disappointment of defeat, Roberto Di Matteo did get to see summer signings Eden Hazard and Marko Marin in action for the Blues on the latest leg of their US tour.
The defeat is Chelsea’s second in succession after losing to the MLS All Stars earlier in the week.