The Potters midfielder was shown a straight red card for an alleged stamp on Jack Cork during the 3-3 draw at the Britannia Stadium.
Stoke boss Tony Pulis was infuriated by the decision, and the club lodged a claim for wrongful dismissal with the Football Association.
A statement from the FA's Independent Regulatory Commission read: "We have upheld a claim of wrongful dismissal in relation to Stoke City's Steven Nzonzi.
"Nzonzi was dismissed for serious foul play during his side's game against Southampton on 29 December 2012.
"The midfielder's three-match suspension has therefore been withdrawn with immediate effect."
Pulis insisted that Cork's reaction to the incident played a major part in Mark Clattenburg's decision to brandish the red card.
He said: "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."