Santos, best known as the Brazilian club where Pele spent nearly all of his career, were fined 75,000 Swiss francs (53,935.37 pounds) while Sevilla were fined 55,000, by FIFA's disciplinary committee.
Brazilian media reported that Santos were investigated over the transfer of Neymar to Barcelona in 2013, although FIFA could not immediately be reached to confirm this.
FIFA said Santos had failed to declare "mandatory information" into its transfer database and failed to co-operate with an investigation.
The other clubs sanctioned were FC Twente from the Netherlands, who were fined 185,000 Swiss francs, and Belgium's St Truiden, fined 60,000.
Sevilla were issued with a warning and the other three clubs with warnings and reprimands.
In all cases, FIFA said that the clubs were "found to be liable for entering into contracts that enabled third parties to influence the club’s independence in employment and transfer-related matters."
FIFA introduced a ban on third-party influence over clubs in 2008.
FIFA statutes state that no club can enter into a contract which allows a third party to influence "in transfer-related matters its independence, its policies or the performance of its teams."
In 2014, FIFA went further and announced that it would ban third-party ownership (TPO), when the transfer rights of players are wholly or partially owned by a company instead of the player's club.
The practice was widespread in Brazil and Argentina and was also present in some European countries such as Spain and Portugal. The ban came into force on May 1 last year.
(Writing by Brian Homewood, editing by Ed Osmond)
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