The sanction was imposed after the club had failed to pay disciplinary fees for making undisclosed payments to players.
The club appealed the IFA Disciplinary Committee decision and hearing is set for the week commencing 15 August.
Portadown's league opener at Coleraine on Saturday could have gone ahead but NIFL said the match remains off.
The Northern Ireland Football League's Premiership Committee added that the decision not to play the game was taken in the best interests of the league.
If the match was allowed to take place, and Portadown's suspension was subsequently reimposed, it could mean the result would be void.
The match will now only be played if Portadown's appeal is successful - if not Coleraine will be awarded the three points.
The fine has now been paid but the IFA Disciplinary Committee did not exercise their discretion to lift the ban at a meeting on Wednesday night.
"Having considered points made by Portadown FC, and taking into account Article 9.3 of the Irish FA's Disciplinary Code as well as being cognisant of Portadown's Premiership game against Coleraine scheduled for this Saturday, they were not persuaded to exercise discretion in this case," said the IFA following Wednesday's meeting.
"The decision means the suspension, which came into effect on Thursday 28th July, will remain in place until the Monday after any payment is made - in accordance with Article 9.3 of the Irish FA's Disciplinary Code."
A fine of £5,000 was handed down in April and it is understood that an initial cheque sent to the IFA 'bounced'.
The fine was imposed, along with a transfer embargo preventing the club from signing players on professional terms until June 2017, after irregularities were found in payments made to former striker Gary Twigg.
Portadown's appeal against a 12-point deduction, imposed after the Shamrock Park club were found to have paid Peter McMahon while he was registered as an amateur, was due to be heard by the IFA's Appeals Committee on Thursday night.
It is understood that the IFA now intend to hear both Portadown appeals at a single meeting.
Portadown's suspension from all football activity has been lifted after the Irish FA said on Thursday that the club has grounds for an appeal.