Coleraine have been deducted three points and fined £350 for playing a suspended player in the Irish Premiership match against Institute.
Ruairi Harkin appeared in Coleraine's 4-0 win on 1 November when he should have been serving a one-match ban.
Coleraine had argued they had not been told when the suspension was effective.
However, Institute will not be awarded the points and have been fined £500 for breaking league rules by including keeper Eugene Ferry in the same match.
In the Premiership, on loan players are not allowed to play against their parent clubs.
Former Derry City player Ferry is currently on loan from Coleraine.
It is expected Coleraine will lodge an appeal against the Irish FA disciplinary committee's decision.
The club added that they had originally brought the matter to the attention of the NI Football League.