It was confirmed prior to Milan's game with Juventus on January 6 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 Monday.
However, Milan revealed on Thursday 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.
"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."