It was confirmed prior to Milan's game with Juventus on 7 January (AEDT) that Rebic and Krunic had tested positive for coronavirus and they have not played since.
Hernandez and Hakan Calhanoglu returned positive results from tests administered last Saturday, ruling them out of the game with Cagliari on Tuesday (AEDT).
However, Milan revealed on Friday that Hernandez's result was a "false positive", while Rebic and Kurnic have now tested negative.
A club statement read: "Milan announces that both Ante Rebic and Rade Krunic underwent a molecular swab test with negative results and this morning had the medical exams required to resume professional activity.
Official Statement: Ante Rebić, Rade Krunić, Theo Hernández ➡ https://t.co/E0YA8yJpSi— AC Milan (@acmilan) January 21, 2021
Comunicato Ufficiale: Ante Rebić, Rade Krunić, Theo Hernández ➡ https://t.co/AyP86qLO99 #SempreMilan pic.twitter.com/1bKqTENzZC
"Further examinations have shown that Theo Hernandez was a 'false positive'. The documentation has been provided to the health authorities and the player can now resume training."
Milan sits top of Serie A with a three-point advantage over local rivals Inter, which it faces in the Coppa Italia next week.
Before that, though, it entertains Atalanta in a league clash at San Siro on Sunday.