Afan Lido, deducted 3 points and fined £100 will appeal to the FAW following the decision by a Welsh Premier in Llandrindod Wells this week, after Lido fielded a suspended player against Airbus UK last month.
With the seaosn due to end next week, it could mean the relegation battle may be decided after the League closes for the summer, until the appeal can be heard.
The Aberavon club, feel harsly treated, saying the ban had not been made known to them with the ban for Leigh Shrimpton coming while playing for a Sunday League side.
Peter Reynolds, press officer for Afan Lido, who attended the hearing on the club's behalf, said: "The chairman of the panel, Alun Evans, admitted there had been poor communication between the South Wales Football Association and the Football Association of Wales and the FAW and ourselves.
"We thought we had presented a good case so we were shocked at the decision."
Lido manager Mark Robinson said: "We are extremely disappointed with the outcome and the fact that we have been ordered to play two matches in two days this weekend makes it worse."
Lido must now also play two games in as many days against Connah's Quay today and fellow strugglers NEWI Cefn Druids tomorrow.
"It makes our job all the harder now, but I'm hoping the events of the week will spur the players on to two great results in
The relegation battle continues...