Inzaghi, 38, is the second-highest scorer in European club competitions with 70 goals, two behind Schalke's Raul.
He missed half of last season's campaign with a knee injury but returned to play in May.
"I hope that Filippo will in good condition in January to be included in the list then," said AC Milan coach Massimiliano Allegri. "I spoke to him and he was disappointed but it's understandable."
Inzaghi was dropped along with injured midfielder Mathieu Flamini.
Milan are in Group H alongside Barcelona, Bate Borisov and FC Viktoria Plzen.