Rebic, who exploded for 11 Serie A goals in the second half of the 2019-20 campaign, signed a five-year contract with the Rossoneri.
Fiorentina, who sold Rebic to Eintracht in 2018 after an initial loan spell, will net around 50% of the transfer fee, according to Sky Sport Italia's Gianluca Di Marzio.
The two sides agreed not to disclose the fee.
Rebic, 26, joined Milan last summer on a two-year loan deal, with Andre Silva heading the other way. Silva enjoyed similar success in the Bundesliga, scoring eight goals in his final 11 appearances of the season, and signed a permanent deal with Eintracht on Thursday.
Before moving to Milan, Rebic helped Eintracht win the DFB-Pokal in 2018, scoring twice in the final against Bayern Munich. He also started six of Croatia's seven matches - including the final against France - at the 2018 World Cup.
"Ante will live long in the memory of our fans, and not only for his outstanding performance in the final of the 2018 DFB Cup," Eintracht board member Fredi Bobic said in a statement. "His displays over this past year have shown that he can establish himself at one of the biggest teams in the world and make the most of the huge amount of potential he has. We agreed to this transfer because we don't want to stand in his way. We wish Ante all the best for the future. He'll always be welcome in Frankfurt."