Morata managed the full 90 minutes away at West Ham at the weekend, but the 25-year-old forward put in a poor performance as the Blues suffered a 1-0 defeat at the London Stadium.
While Morata was understood to be ill in the lead-up to Saturday’s clash, the Spaniard will miss the trip to the John Smith’s Stadium after picking up a back injury.
Danny Drinkwater, though, who has only made six Premier League appearances since his summer transfer, has returned to training.
Asked about Chelsea’s team news, Conte said: ‘Drinkwater started a training session yesterday after the fever and is coming with us.
‘But, for sure, after three or four days with a fever, his physical condition is not at the top.
‘[David] Luiz is continuing to recover from his knee.
‘Morata is out, because he’s a bit tired and there is a problem in his back. He is out.’
Conte will be desperate for the striker to return to action, with Chelsea facing Southampton, Bournemouth, Everton, Brighton and Stoke before the end of the month.
Chelsea 2017/18 Fixtures
Huddersfield Town (A) – Tues Dec 12
Southampton (H) – Sat Dec 16
Bournemouth (H) – Wed Dec 20 (EFL Cup)
Everton (A) – Sat Dec 23
Brighton (H) – Tues Dec 26
Stoke City (H) – Sat Dec 30