This fixture kicks off at the Gewiss Stadium in Bergamo on Saturday at 17.00 GMT.
The Portugal international returned to training this week and tests showed that the lesion in his thigh muscle had completely healed.
He sustained the injury during the opening minutes of the 2-2 draw against Lecce on November 11, missing games with Borussia Dortmund, Fiorentina and Frosinone.
It was believed that Leao would at least be on the bench for this weekend’s trip to Atalanta, a head-to-head for the top four places.
However, Stefano Pioli and the medical staff decided it would be best to let him continue training at Milanello and make a full recovery ahead of the crucial Champions League trip to Newcastle.
Leao has contributed four goals and as many assists in 16 competitive games for Milan this season.
Simon Kjaer, Noah Okafor, Malick Thiaw, Marco Pellegrino, Mattia Caldara, Pierre Kalulu and Marco Sportiello are also out of the Atalanta match.
Olivier Giroud does return from a two-match Serie A ban.