"Both Rebic and Krunic underwent a molecular swab test with negative results and this morning had the medical exams required to resume professional activity," AC Milan said.
Croatian forward Rebic and Bosnian midfielder Krunic have been out since January 6, with France's Hernandez and Turkish midfielder Hakan Calhanoglu both testing positive last weekend.
"Further examinations have shown that Theo Hernandez was a 'false positive', the team added. "The documentation has been provided to the health authorities and the player can now resume training."
Milan host Atalanta on Sunday looking to maintain their lead on top of the Serie A table ahead of second-placed city rivals Inter.