Hazard missed three matches with a back problem before returning as a substitute in Sunday's Premier League win over Crystal Palace, but has made the journey to Belarus for the Group L fixture at Borisov Arena.
Morata scored twice against Palace, but Blues head coach Maurizio Sarri has opted to rest his in-form striker.
"He played for three matches in a row. I thought it was better for him to stay at Cobham and rest and have only training," said Sarri, speaking in Minsk.
Cesc Fabregas was a late withdrawal through illness, resulting in N'Golo Kante travelling.
Sarri wants Hazard to get some additional match action, after his return last Sunday, and insisted the flight was not a problem for the Belgian.
"For our doctor, there is not any risk, otherwise he would stay in Cobham, of course. We thought for him it's better to play, not for 90 minutes, but to play after two weeks without training.
"In the last match he played only for 30 minutes. Tomorrow the best for him is he will play 45, 50 minutes."
Chelsea will be confirmed in first place with two rounds of matches to go if they win and the other game, between Vidi and PAOK in Budapest, is drawn.
Midfielder Mateo Kovacic is cautioning against complacency, though, after watching Liverpool fall to defeat at Red Star Belgrade in the Champions League on Tuesday night.
"I watched the game, Liverpool struggled a lot," the on-loan Real Madrid midfielder said.
"In Belgrade, the atmosphere is tough. It's difficult to play there, like here. These are games where you need to concentrate a lot or you will lose the game.
"The most important thing is we need to be prepared so that what happened to Liverpool doesn't happen to us."
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