The Allievi will play Sao Paulo on Friday.
The goals all came in the second half and were scored by Zucchetti and two from Agnero.
Milan will now play Sao Paulo on Friday with the kick-off at 13.35 CET.
The Rossoneri had to battle for victory but they came through despite injury to Altare but Agnero took his goal tally to five so far.
took his goal tally to five so far.