During Liverpool's 1-0 victory over Manchester City on October 16, Klopp was shown a red card for confronting the official after Mohamed Salah was denied a free kick.
Klopp, who later apologised for his outburst, had initially been fined £30 000 after accepting an improper conduct charge but the FA appealed against the punishment handed out by an independent regulatory commission.
"As a result, the Liverpool FC manager has been suspended from the touchline for one match with immediate effect... and warned as to his future conduct," the FA said in a statement.
Liverpool are eighth in the standings with 19 points from as many games while Southampton are 18th with 12 points, having played a game more.
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