Napoli had made an approach for the Italy international in January but their offer was turned down.
"It is a true privilege," Roberto La Florio told Radio Kiss Kiss. "But it seems to me that Milan have made a long-term investment with Stephan.
"The Rossoneri are re-building, but they have some good young players. Stephan has a contract until 2018."
The 20-year-old has scored 16 goals in 32 Serie A appearances so far this season.