Portsmouth were fined 15,000 pounds ($22,570) with a further 15,000-pound fine suspended for two years following the investigation by an independent regulatory commission.
Scotland-registered agent Willie McKay was given a suspended suspension of his overseas registration.
Portsmouth issued a statement on their website saying the club was "astounded" by the findings.
"We had no idea that Willie McKay received a fee when Benjani joined us from Auxerre," the club said.
"Both the agent and the club confirmed this to the FA - evidence they have clearly ignored."
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