Sakho withdrew from the tournament in Equatorial Guinea due to a back problem, but came on as a substitute to score the winner in West Ham's FA Cup fourth round tie at Bristol City before his country were knocked out of the AFCON.
The Senegal Football Federation lodged a complaint with FIFA after hearing of Sakho's involvement in that match and coach Alain Giresse claimed West Ham had set a "dangerous precedent" by opting to select the 25-year-old.
West Ham boss Sam Allardyce and co-owner David Sullivan stated that they do not expect Sakho to be banned by the world governing body.
But FIFA on Monday confirmed that it had opened proceedings against the London club and the former Metz man, who did not feature in Saturday's Premier League defeat at Liverpool.
A FIFA spokesman said: "We can confirm that disciplinary proceedings were initiated against the player Diafra Sakho and the club West Ham United for a potential violation of the FIFA Regulations on the Status and Transfer of Players."
Sakho spoke of his "sadness and anger" after Senegal fans vented their fury at him for missing the AFCON, in which Giresse's side failed to qualify from Group C.
While Allardyce stated ahead of the trip to Liverpool: "I'm not worried that Sakho will face a ban whatsoever.
"We have stuck by every rule and regulation in the book."
West Ham now face an anxious wait to discover what action, if any, FIFA opts to take.
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