Portadown have lost their appeal against a 12-point deduction while Coleraine have been awarded a 3-0 win from the postponed Premiership fixture between the clubs on 6 August.
The Coleraine game was postponed after Portadown were suspended from all football activity for the non-payment of a £5,000 fine.
Portadown were found to have made irregular payments to players.
An IFA appeals board rejected the club's appeal against both penalties.
The IFA appeals board's decision means Portadown remain rooted to the bottom of the Premiership on minus six points while Coleraine's three additional points moves them from fifth to third spot in the table above Cliftonville and Ballymena United.
Portadown attempted to 'deceive IFA'
In his judgement, appeals board chairman Joseph McCrisken accused Portadown of a "breathtaking breach of sporting integrity" and said their attempts to "deceive the Irish FA" by altering the contract documents of former player Peter McMahon "potentially constituted a criminal offence".
The club's 12-point deduction was imposed after they were found to have paid McMahon while he was registered as an amateur.
In late August, Portadown were also ordered to pay £7,000 in unpaid wages to McMahon by an employment tribunal although the club said that they would be appealing against this verdict.
"It is our view that, in the case of Peter McMahon, Portadown did not act with the transparency and integrity which was expected of them," said the appeals board chairman.
"Instead representatives from the club signed a player on a contract which was not dated, then at a later stage amended the contract by writing over some of the characters and scribbling out others so that the IFA would think that the player was not being paid for 6 months when he in fact was.
"Not only does this potentially constitute a criminal offence but is a breathtaking breach of sporting integrity.
"The evidence presented by Portadown to the appeal lacked any real credibility.
"The club representatives said that they were unable to tell us who the mystery person was that had amended the contract and sought to deceive the IFA.
"Accordingly, we have no hesitation in finding, as the disciplinary committee did, that by sending the IFA a redacted contract which did not disclose that the player was being paid as a professional, that Portadown not only breached Rule 38(a) but also brought the game of football into disrepute in breach."
Portadown's subsequent suspension from all football activity was imposed for the non-payment of a £5,000 fine and Tuesday's judgements gives a detailed timeline on the IFA's attempts arrange collection of the financial penalty.
Portadown cheque bounced
This included details of a cheque for £3,000 from Portadown bouncing after it had been given to the IFA on 22 July which ultimately led to the club's suspension.
Portadown's outstanding fines were all paid on Friday, 5 August, one day before their scheduled opening fixture with Coleraine but under IFA rules, such suspensions remain in place until the Monday after fines are paid.
"It is clear from the wording of Article 8 that neither the disciplinary committee, nor the disciplinary manager, enjoys discretion to remove a suspension once it has been imposed," continued the judgement.
"Article 13 of the articles of association does not provide discretion, contrary to the legal advice given to the disciplinary committee.
"Accordingly, since Portadown paid the outstanding fines on 5 August the suspension should have remained effective until 8 August 2016.
"Since Portadown had a game against Coleraine on 6 August that match is forfeited and the tie awarded to Coleraine with a score of 3-0."
Following Tuesday's judgements, the Northern Ireland Football League said that its management committee will now meet to discuss the financial impact on Coleraine of the postponement of the opening game of the season, which had been scheduled for the Showgrounds.
Saturday's scheduled fixture between Portadown and Coleraine will go ahead at Shamrock Park, with a 17:30 BST kick-off.