The Italy international has made four appearances so far this season, scoring one goal, and has struggled in recent times with a thigh strain, his last outing for the club coming in the 3-1 win over Cagliari on September 1.
El Shaarawy had been due to make his return to the side for their UEFA Champions League clash with Ajax on Tuesday, but he will now miss out after sustaining a hairline fracture in his left foot.
Milan have not revealed how long the 20-year-old will be unavailable for, although there is some good news for manager Massimiliano Allegri, with midfielder Ricardo Montolivo poised to make his comeback.
The former Fiorentina man has not played since the 2-2 draw with Torino on September 14 because of a thigh problem, but has been named in the squad for the trip to the Netherlands.
Milan head into the game at the Amsterdam Arena having ended a three game winless streak in Serie A with a 1-0 success over Sampdoria on Saturday.
Allegri's men were 2-0 victors over Celtic in their opening match of the Champions League, an own-goal from Emilio Izaguirre and a Sulley Muntari strike giving them the points.
They meet an Ajax side dismantled 4-0 by Barcelona in their first game and, despite the absence of El Shaarawy, Allegri will know they can put themselves in a strong position to qualify from the group with a win.
