The 21-year-old rising star is currently owned by his Serie B club and Parma, but he is expected to move to the San Siro in the summer.
Milan vice-president Adriano Galliani and head coach Massimiliano Allegri are currently in the process of bringing down the age of the squad, which the club seem highly satisfied with.
Saponara told reporters: "I can't believe it that I'm actually joining Milan. I had just finished training and then my team-mates congratulated me.
"I read the news about Milan having signed me and I couldn't believe it. I immediately started crying out of joy.
"Joining Milan is a great dream come true for me. It means that all the sacrifices have been worth it.
"I feel a great sense of responsibility after this transfer. Now I just want to finish the season with Empoli in the best way."