Nzonzi was sent off for an alleged stamp on Southampton's Jack Cork during a thrilling 3-3 Premier League draw at the Britannia Stadium.
Potters boss Tony Pulis was angered by Mark Clattenburg's decision, arguing that Nzonzi did not make contact with Cork.
The Football Association have confirmed an appeal has now been lodged and Stoke have until 1pm on Wednesday to submit evidence.
If the appeal is rejected, Nzonzi will face a ban of at least three matches.
Pulis, who felt Cork overreacted, said of the incident: "Whether the reaction of Cork, who is a good player and a good lad, has influenced Mark, I'm not sure, but Steven certainly doesn't stamp on the player.
"There was no intent. He's actually planted his leg between his legs, which was quite clever."