The commission found the club guilty of unacceptable conduct over a series of issues surrounding last season's play-off match against Rangers on 31 May.
The SPFL, however, delayed punishment for 18 months.
Now Motherwell have urged fans not to enter the pitch or trackside "at any game in future", home or away.
Supporters invaded the pitch after Well beat Rangers 3-0 in the Premiership play-off final second leg, which completed a 6-1 aggregate victory for the Steelmen and preserved their top-flight status.
A statement on the club's website read: "Although much of what is required of the club by the commission is being addressed by the club, it is important to emphasise the role of our supporters in helping meet the requirements of the commission.
"While the club acknowledges that the end of season pitch incursions at Fir Park, by predominantly young supporters, have almost always been celebratory and without malice, incursions themselves are considered to be 'unacceptable conduct' and may give rise to further disorder.
"In particular, the incursion on 31 May 2015 was found to be disorderly by the commission.
"It is clear that the league will no longer accept these incursions and the club could face extremely serious sanctions should there be a repeat.
"It is absolutely paramount that no fan enters the pitch or trackside area at any game in future, either at Fir Park or elsewhere.
"Should this instruction be ignored, the club will reluctantly be left with no other option but to take appropriate action against those concerned, which may include a significant ban from the stadium."
The club insisted it is "immensely proud of its supporters".
"We would ask supporters take heed of the message and work with us to ensure no further issues or problems," the statement added.
"In return, the club will continue to work hard for supporters' rights and the often valid concerns that are frequently raised in response."
Motherwell have warned supporters against pitch incursions at Fir Park following a Scottish Professional Football League commission ruling.