Morata, who was suspended for the Blues' 4-0 win over Brighton & Hove Albion at the weekend, misses out on the trip to the Emirates Stadium due to a minor back problem.
Former Arsenal midfielder Fabregas is absent because of a hamstring strain, meanwhile, which also kept him out of the games against Norwich City and Brighton.
Speaking to reporters ahead of Wednesday evening's clash, Conte said: "Morata and Fabregas are out. They are not available for the Arsenal game. Then I have to check a couple of situations [with other players]."
The sides are locked at 0-0 following their stalemate in West London a fortnight ago.