The Scotland international apologised the following day for the incident and claimed he had only meant to remove the item from the pitch after it was thrown on following a Saints goal in the away side's 2-0 win on September 22.
Griffiths was charged by Police Scotland in relation to "culpable and reckless" conduct and now the SFA has also charged the 31-year-old striker, on loan from Celtic, for bringing the game into disrepute and acting in a manner which is improper and not in the best interests of the game.
In his statement released on Dundee's official website the day after the incident, Griffiths said: "It was regrettable that the pyrotechnic ended up back in the stand as my intention was just to remove it from the pitch.
"Having just lost a goal I was eager to get the match restarted as quickly as possible and I would like to apologise for any distress caused by this action."
The principal hearing for the case is on Thursday, October 14.
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