Southampton players mobbed referee Mark Clattenburg when he pointed to the spot in the third minute of stoppage time of their 0-0 draw at Norwich City last weekend.
The referee decided Southampton's Luke Shaw had fouled Grant Holt, who then had his penalty superbly saved by keeper Artur Boruc.
"The FA has today fined Southampton £20,000 after they admitted a charge of failing to control their players," English football's governing body said in a statement.
Southampton are 16th in the Premier League, four points clear of the relegation zone.
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