The Potters' man was sent off by match official Mark Clattenburg after a challenge on Saints' midfielder Jack Cork in their match on Dec. 29, however replays suggested there was little, if any, contact.
His manager, Tony Pulis, was furious with the decision after the clash, insisting his player did not stamp on the opponent and the tackle showed no "intent", before the club lodged an official appeal.
The former Blackburn midfielder has now been cleared of any wrongdoing, and has had his three-match suspension lifted.
A statement on the FA's official website reads: "An Independent Regulatory Commission has today 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 December 29 2012.
"The midfielder's three-match suspension has therefore been withdrawn with immediate effect."
The decision means the 24-year-old will now be available for the Potters' FA Cup tie with Crystal Palace on Saturday as well as their following league matches with Chelsea and Swansea. Nzonzi was eligible for their game against Manchester City on Tuesday, which the team lost 3-0.