Chelsea make the trip to Emirates Stadium hoping to book a place in the final, with the goalless draw in the first leg teeing up the return match perfectly.
But Morata, who missed Saturday's 4-0 win over Brighton and Hove Albion through suspension, will be forced to sit out once again due to injury.
And Fabregas is still nursing a hamstring injury, meaning he will be unable to feature against his former team.
Speaking to reporters at his pre-match news conference on Tuesday, Conte said: "Morata has a problem in his back and is injured.
Antonio Conte reports that Alvaro Morata and Cesc Fabregas are out of tomorrow's game. Morata has a problem with his back. A couple of other players will be checked before the game. — Chelsea FC (@ChelseaFC) January 23, 2018
"Morata and Fabregas are definitely out, they're not available for us. Then I have to check a couple of situations [in terms of injuries to other players]."
Arsenal will, of course, be without the services of Alexis Sanchez following his move to Manchester United, but they will also be unable to call upon the cup-tied Henrikh Mkhitaryan, who came the other way in the deal.
Conte does not think those absences will have any impact on the match, however, highlighting that Arsenal were also without Sanchez in previous meetings with Chelsea.
"I think Arsenal has a good squad," Conte said. "If you remember the game at home in the league, Sanchez didn't play.
"The same in the EFL Cup, he only played 10 minutes. I don't see any advantage about this situation."
Chelsea find themselves within one match of returning to Wembley and, for Conte, the chance of reaching another final within two years of joining the club is an exciting one.
"For me, my players, for the fans, it's an important target, especially for me," he said.
"To have this possibility to play many finals in this country, it is very important for me. To play the final we must get past Arsenal, which is always a big challenge. Arsenal will also want to go to the final."