The young Brazilian was expected to start in the fourth round encounter after making his debut in the Premier League win against Brighton in midweek.
However, the Birmingham Mail says Alysson picked up a knock in training on Friday, with Emery deciding against risking him for the tie.
The injury is described as "small", with Emery determined to manage the 19 year-old's introduction to English football. The winger joined Villa last month from Gremio.
“He’s a winger. Left foot winger playing normally on the right side, and (he) can play in the left side, but normally he’s playing on the right side,” Emery said on Friday.
“He has qualities or skills like, more or less, Leon Bailey – left foot playing in the right side, and he has a huge potential.
“Of course, his adaptation is being progressively better, but he needed time, and he is still needing time to adapt of us, and to get his best performances.
“But each match or each training session is very important for him.”