Several hundred home supporters ran on to the Fir Park pitch after Motherwell’s 3-0 second-leg win on May 31, which clinched a 6-1 aggregate victory.
Many ran in the direction of the away stand to taunt the Rangers fans before returning to the stands as police horses prepared to enter the field.
SPFL chief executive Neil Doncaster announced earlier this week that the league body was considering action.
In a statement it said: “The SPFL has today announced it has charged Motherwell FC with alleged breaches of SPFL Rules in relation to alleged Unacceptable Conduct on the occasion of the Premiership/Championship Play-Off Final Match at Fir Park on Sunday 31 May 2015.
“The charges relate to aspects of match organisation, security arrangements and supporter organisation. They do not concern aspects of player behaviour which have been dealt with by the Scottish FA.
“A Commission chaired by an independent senior solicitor will hear the case.”
The Scottish Football Association has already dealt with a brawl involving players.
Former Rangers defender Bilel Mohsni, who has now signed for French Ligue 1 side Angers, was banned for seven games while Motherwell players Craig Moore, Lionel Ainsworth and Fraser Kerr were given two-match suspensions.