Rui Costa's late strike for the Serie A outfit cancelled out Didier Drogba's opener for Chelsea and meant Jose Mourinho's side were unable to make it three wins from three on their US tour.
But earlier results against Milan and DC United were enough to ensure success in the tournament, in what has been an encouraging build-up to the new Barclays Premiership campaign for the English champions.
Having already lost 1-0 to Chelsea earlier in the tour, Milan were eager to level matters and were already pressing their opponents in the early stages.
Albert Gilardino, a recent signing from Parma, showed some promising form for his new team after just two minutes, beating the Chelsea offside trap before sweeping his shot past the left post.
And the Chelsea backline was exposed again nine minutes later with Gennaro Gattuso finding Cafu down the right, allowing the Brazilian to charge at his opponents.
However, a goal failed to materialise as the defender also pushed his effort past the wrong side of the upright.
The English champions were struggling to find any openings with the Milan midfield not afraid to challenge the likes of Frank Lampard and Eidur Gudjohnsen in the middle of the pitch.
And the Italians' persistence almost paid off after 27 minutes when another promising build-up saw Georgian international Kakha Kaladze flash a shot from the right across the face of the Chelsea goal.
Chelsea finally caught a glimpse of the Milan net after 35 minutes with Joe Cole winning a free-kick on the edge of the penalty area, but new-boy Asier Del Horno curled the ball inches over the crossbar.
And Milan quickly re-asserted their authority on the game with Chelsea needing a swift intervention from John Terry shortly after the interval as the Italians once more threatened to overrun the Blues defence.
The London club then lost both William Gallas and Claude Makelele to injury, but in the 64th minute substitute Drogba finally gave Chelsea something to smile about as the Frenchman powered his way past Gattuso before sweeping the ball home.
Milan then looked to have pulled level six minutes later when a free-kick from Andrea Pirlo came back off the crossbar and was turned in by Christian Vieri, but the goal was disallowed with the Italian striker deemed to be in an offside position.
But the Italians eventually made the breakthrough 10 minutes from time with Portuguese midfielder Rui Costa curling a delightful ball over Petr Cech and into the net.
Chelsea (4-3-3): Cudicini (Cech, h-t); Ferreira (Carvalho, h-t), Terry, Gallas (Johnson, 54), Del Horno; Gudjohnsen (Geremi, 69), Makelele (Tiago, 60), Lampard; Duff, Crespo (Drogba, h-t), J Cole (Wright-Phillips,h-t). Substitutes not used: Huth.
Milan (4-4-2): Eleftheropoulos (Fiori, h-t); Cafu, Nesta, Stam (Costacurta, h-t), Kaladze; Ambrosini, Gattuso (Vogel, 68), Seedorf (Rui Costa, h-t), Pirlo; Vieri, Gilardino. Substitutes not used: Marzoratti, Serginho, Ardemagni.Reuse content