The 24-year-old was cited for appearing to head-butt Hamill in the first half of their side’s 4-1 win which secured their top- flight status after Hamill had criticised the striker for conceding a free-kick.
Both players and Killie manager Gary Locke dismissed the incident but a notice on the SFA’s website said Magennis had breached Disciplinary Rule 200, with the Northern Irishman being offered an immediate two-match ban by compliance officer Tony McGlennan.
The notice said: “In that at the above match you committed an offence listed in the Schedule of Offences contained in Section 3 of Annex C to the Judicial Panel Protocol, namely A2 Violent Conduct, by head-butting Jamie Hamill of Kilmarnock FC.”
Magennis has until 3pm on Wednesday, May 20 to respond to the complaint.
Elsewhere, Motherwell should learn on Thursday if Scott McDonald’s appeal for wrongful dismissal has been successful.
The striker was shown a red card for an alleged elbow during his side’s defeat to St Mirren at the weekend.
If upheld, McDonald would miss the first leg of his side’s play-off final against either Rangers or Hibernian.