The Dundee striker, on loan from Celtic, was filmed taking aim and booting a lit flare back into a crowd of St Johnstone fans after it had been thrown onto the pitch.
The Scotland international declared he had only meant to remove the item from the pitch after it was thrown on following a goal for the visitors at Dens Park.
The 31-year-old apologised in a joint statement with his on-loan club, with Dundee branding the incident 'regrettable'.
Following the game, Police Scotland said they were investigating the incident, although stated there were no injuries as a result of the player's actions, and no complaints were reported at the time.
And the force has now confirmed Griffiths has been charged with 'culpable and reckless conduct'.
Griffiths could also face Scottish Football Association disciplinary action but the police charge could delay that process.
A Police Scotland spokesperson said: "Police Scotland can confirm that a 31-year-old man has been charged in relation to culpable and reckless conduct, following an incident at Dens Park, Dundee, on Wednesday, September 22. A report will be submitted to the Procurator Fiscal."
The incident - which happened shortly after Shaun Rooney had scored the opening goal in St Johnstone's 2-0 victory in the Premier Sports Cup quarter-finals - was filmed by a supporter and posted on social media.
Dundee issued a statement on Thursday in which Griffiths apologised for his actions.
It read: "Dundee Football Club and Leigh Griffiths would like to address a regrettable incident which occurred during last night's Premier Sports Cup tie with St Johnstone at the Kilmac Stadium.
"Following the opening goal a smoke generator, among other items, was thrown onto the park by the visiting supporters. This pyrotechnic ended up back in the stand as Leigh kicked it to remove it from the field of play."
Griffiths, who recently returned to Dundee on loan from Celtic, added: "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."
Dundee host Rangers in the cinch Premiership on Saturday.