The 24-year-old has scored six goals in seven league games so far this season, but picked up a hamstring injury in the 1-0 home loss to Manchester City just before the international break.
Conte has now confirmed that the Spaniard will miss the trip to Selhurst Park, along with Danny Drinkwater and N'Golo Kante, but will be back in contention for the home encounter with Roma in the Champions League four days later.
"As you know very well, we have three injured players," Conte told reporters at his pre-match presser this afternoon. "[With] Morata, I hope to have him back very soon - I hope for the next game against Roma.
"Drinkwater is progressing well but is not ready yet. We must have patience with him and his calf problem.
"Then the last is Kante. We are going to do a scan next week to check his situation. He is improving but for sure he has a hamstring problem. This is a big loss for us."
The Blues go into the game fourth in the table, six points behind leaders City.