FIFA said Independiente had been fined 35,000 Swiss francs for charging Genoa a fee to provide a document known as the International Transfer Certificate (ITC) which should have been issued free of charge.
The Serie A club were penalised the same amount for "failing to submit information and upload relevant documents into TMS (Transfer Matching System) once the transfer contract had been signed".
The player involved was Julian Alberto Velazquez, FIFA said. The transfer has stalled and the 22-year-old is still with Independiente.
All international transfers have to be conducted through a web-based system known as TMS, introduced by FIFA in 2010 to provide greater transparency and crack down on money laundering and third-party ownership of players.
Before that, international transfers were carried out by faxes between the national associations involved, a system which FIFA say was open to all kinds of abuse.
To complete a transfer using TMS, both the buying and selling clubs must enter details into the system including the transfer fee, the player's salary, the agent or lawyer involved and the length of the contract.
The money must be transferred from and to a bank account.
FIFA said that Independiente could face further sanctions for failing to authorise the transfer.
"Conditioning the issuance of the ITC is a serious breach of the regulations," said FIFA's disciplinary committee in announcing the decision.
"(It) jeopardises the transparency of international transfers, stains the credibility of the entire transfer system and hinders the possibility of the football authorities to have a more effective monitoring of international transfers.
"Players' activities are hindered and prejudiced by such behaviour.
"The use of TMS is obligatory. Its purpose is to ensure that football authorities have clear details of the international transfers of players available, and thus improve credibility and transparency of the system."