Portadown have had their fine for undisclosed player payments halved to £5,000 on appeal but a signing ban until next June remains in place.
The Irish FA ruled that the club concealed the fact that Gary Twigg was to be paid an extra 14 weeks wages.
However, the appeal against the charge of making undisclosed payments to Tim Mouncey was allowed.
"It is a fair and proportionate punishment for the offence of bringing the game into disrepute," said the IFA.
It added: "We do not consider that expelling Portadown from the Danske Premiership, relegating them or forfeiting points would be a proportionate or fair punishment for this particular offence.
"However, the offence committed by Portadown must be treated as a serious breach of sporting integrity."
The signing ban relates to players on a new professional contract until 1 June, 2017.
Portadown have responded to Friday's decision by saying that the punishment "for this minor oversight is wholly disproportionate and detrimental to the future of the club".
"We will consult with our legal advisors as to the options available to challenge the severity of the punishment."
Portadown have endured a troubled season, with long-standing manager Ronnie McFall stepping down from his position last month after 29 years in charge.
The club head into the final round of Irish Premiership fixtures this weekend still under threat of relegation in ninth place and only three points ahead of bottom-placed Carrick Rangers.