The Durham official angered Saints when, during their defeat to Everton on December 29, he told captain Adam Lallana: "You are very different now, since you've played for England - you never used to be like this."
The club reported those comments to referees' governing body PGMOL and insisted it would be difficult for Clattenburg to take charge of their matches in future, but the referee was cleared of any wrongdoing.
Clattenburg was previously cleared of a complaint by Chelsea that he racially abused their player John Obi Mikel and has since taken charge of games involving the London club.
The latest complaint was also dismissed after investigation by PGMOL and the Football Association.
An FA statement last month read: "The FA can confirm it received a complaint from Southampton concerning referee Mark Clattenburg and his alleged comments made to their player Adam Lallana.
"The FA has given its full consideration to this matter and it is our view that the comments, as disclosed in Southampton's letter of complaint, do not constitute misconduct under the FA's rules.
"Consequently, The FA will not be taking any further action in relation to this matter and now considers this case to be closed."