Morata was brought off in the first half of the Europa League dead rubber after injuring himself while attempting to latch on to Callum Hudson-Odoi’s cross.
However, Kepa Arrizabalaga, Antonio Rudiger, Eden Hazard, Cesar Azpilicueta and N'Golo Kante are all likely to start on Sunday having been rested for the trip to Hungary.
Mateo Kovacic, Gary Cahill and Victor Moses are also likely to miss out.
Chelsea’s weakened side came 15 minutes from a shock defeat against Vidi, before Olivier Giroud’s fabulous late free-kick rescued his Maurizio Sarri's side from an embarrassing defeat.
However, the clash was marred by alleged antisemitic chanting from Chelsea’s travelling fans, overshadowing the build-up to Sunday's fixture.
A Chelsea club spokesman released an exasperated statement during the match:
"Anti-Semitism and any other kind of race-related or religious hatred is abhorrent to this club and the overwhelming majority of our fans. It has no place at Chelsea or in any of our communities.
"We have stated this loud and clear on many occasions from the owner, the board, coaches and players.
"Any individuals that can't summon the brainpower to comprehend this simple message and are found to have shamed the club by used using anti-Semitic or racist words or actions will face the strongest possible action from the club."
Provisional squad vs Brighton: Kepa, Caballero, Rudiger, Alonso, Fabregas, Jorginho, Kante, Barkley, Hazard, Pedro, Loftus-Cheek, Giroud, Zappacosta, Willian, Christensen, Azpilicueta, Morata, Luiz, Emerson Palmieri, Ampadu, Hudson-Odoi.
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