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.
It was found that McKay acted on behalf of AJ Auxerre in the transfer of Benjani from the French club to Portsmouth in January 2006 and then on behalf of Portsmouth when Benjani moved to Manchester City two years later.
FA regulations prohibit agents from acting for two different clubs in two consecutive transactions involving the same player.
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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